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A CPU of a rounding imaging management apparatus functions as a first acquisition unit, a second acquisition unit, a creation unit, and an output controller. The first acquisition unit acquires imaging order information indicating content of radiography in the rounding imaging to be performed. The second acquisition unit acquires, from time results data in which a necessary time in the rounding imaging performed in the past is registered, the necessary time. The creation unit creates a rounding plan of the rounding imaging on the basis of the imaging order information and the necessary time. The output controller performs a control for outputting the rounding plan.
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1. A rounding imaging management apparatus that manages rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus, comprising:
a first acquisition unit that acquires imaging order information indicating content of the radiography in the rounding imaging to be performed; a second acquisition unit that acquires, from time results data in which a necessary time in the rounding imaging performed in the past is registered, the necessary time; a creation unit that creates a rounding plan of the rounding imaging on the basis of the imaging order information and the necessary time; and an output controller that performs a control for outputting the rounding plan. 2. The rounding imaging management apparatus according to claim 1,
wherein the rounding plan includes a rounding route of the mobile radiography apparatus. 3. The rounding imaging management apparatus according to claim 2,
wherein an individual necessary time taken for each past radiography is registered as the necessary time in the time results data, wherein the second acquisition unit acquires the individual necessary time corresponding to the radiography indicated by the imaging order information, and wherein the rounding plan includes a predicted total necessary time that is calculated on the basis of the individual necessary time and predicted to be taken for the entire rounding imaging. 4. The rounding imaging management apparatus according to claim 3,
wherein the individual necessary time is at least one of an imaging time of the radiography or a movement time of the mobile radiography apparatus, and wherein the time results data is at least one of imaging time results data in which the imaging time is registered or movement time results data in which the movement time is registered. 5. The rounding imaging management apparatus according to claim 3,
wherein the imaging time results data is data in which a time slot and the individual necessary time are registered in association with each other, and the individual necessary time varies according to the time slot, and wherein the creation unit creates a shortest time route where the predicted total necessary time becomes the shortest as the rounding route. 6. The rounding imaging management apparatus according to claim 5,
wherein the imaging order information includes hospital room information of the hospital room of the patient for whom the rounding imaging is to be performed, and wherein the creation unit creates a shortest distance route where a movement distance of the mobile radiography apparatus becomes the shortest on the basis of the hospital room information, and then, corrects the shortest distance route in accordance with the individual necessary time to create the shortest time route. 7. The rounding imaging management apparatus according to claim 5, further comprising:
a third acquisition unit that acquires patient schedule information in which a schedule of treatment for the patient is registered, wherein the creation unit creates the shortest time route with reference to the patient schedule information. 8. The rounding imaging management apparatus according to claim 5, further comprising:
a fourth acquisition unit that acquires assistant schedule information in which a schedule of an assistant who assists the radiography is registered, wherein the creation unit creates the shortest time route with reference to the assistant schedule information. 9. The rounding imaging management apparatus according to claim 5, further comprising:
a fifth acquisition unit that acquires current status information indicating a current status of information that is a source of creation of the rounding plan during the rounding imaging based on the shortest time route; and an updating unit that updates the shortest time route and sets the updated shortest time route in a case where the current status information includes content which changes the individual necessary time, wherein the output controller outputs the updated shortest time route. 10. The rounding imaging management apparatus according to claim 9,
wherein the current status information is at least one of room occupancy status information indicating a room occupancy status in the hospital room of the patient for whom the rounding imaging is to be performed, treatment status information indicating a status of treatment in the hospital room of the patient for whom the rounding imaging is to be performed, availability status information indicating an availability status of an assistant who assists the radiography, or congestion level information indicating a congestion level of a hospital. 11. The rounding imaging management apparatus according to claim 10, further comprising:
a first estimation unit that estimates an absence time of the patient indicated as being absent in the room occupancy status information, wherein the updating unit updates the shortest time route on the basis of the absence time estimated by the first estimation unit. 12. The rounding imaging management apparatus according to claim 10, further comprising:
a second estimation unit that estimates, in a case where the treatment status information indicates that the treatment is performed in the hospital room, a treatment time to be taken for the treatment, wherein the updating unit updates the shortest time route on the basis of the treatment time estimated by the second estimation unit. 13. The rounding imaging management apparatus according to claim 3, comprising:
a reception unit that receives, in a case where an actual total necessary time in a case where the rounding imaging is actually performed in accordance with the rounding plan is delayed by a set time or longer from the predicted total necessary time, delay cause information indicating a cause of the delay of the actual total necessary time; and a recording controller that performs a control for recording the delay cause information in a storage unit. 14. The rounding imaging management apparatus according to claim 1,
wherein the output controller performs a control for outputting a scheduled start time of the radiography based on the rounding plan. 15. A method for operating a rounding imaging management apparatus that manages rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus, comprising:
acquiring imaging order information indicating content of the radiography in the rounding imaging to be performed; acquiring, from time results data in which a necessary time in the rounding imaging performed in the past is registered, the necessary time; creating a rounding plan of the rounding imaging on the basis of the imaging order information and the necessary time; and performing a control for outputting the rounding plan. 16. A non-transitory computer-readable storage medium storing a program for operating rounding imaging management apparatus that manages rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus, the program causing a computer to function as:
a first acquisition unit that acquires imaging order information indicating content of the radiography in the rounding imaging to be performed; a second acquisition unit that acquires, from time results data in which a necessary time in the rounding imaging performed in the past is registered, the necessary time; a creation unit that creates a rounding plan of the rounding imaging on the basis of the imaging order information and the necessary time; and an output controller that performs a control for outputting the rounding plan. 17. Anon-transitory computer-readable storage medium storing a data structure in which a necessary time in rounding imaging performed in the past is registered, in order to manage the rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus. 18. A recording apparatus comprising a recording controller that records a necessary time in rounding imaging performed in the past is stored in a storage unit, in order to manage the rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus.
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A CPU of a rounding imaging management apparatus functions as a first acquisition unit, a second acquisition unit, a creation unit, and an output controller. The first acquisition unit acquires imaging order information indicating content of radiography in the rounding imaging to be performed. The second acquisition unit acquires, from time results data in which a necessary time in the rounding imaging performed in the past is registered, the necessary time. The creation unit creates a rounding plan of the rounding imaging on the basis of the imaging order information and the necessary time. The output controller performs a control for outputting the rounding plan.1. A rounding imaging management apparatus that manages rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus, comprising:
a first acquisition unit that acquires imaging order information indicating content of the radiography in the rounding imaging to be performed; a second acquisition unit that acquires, from time results data in which a necessary time in the rounding imaging performed in the past is registered, the necessary time; a creation unit that creates a rounding plan of the rounding imaging on the basis of the imaging order information and the necessary time; and an output controller that performs a control for outputting the rounding plan. 2. The rounding imaging management apparatus according to claim 1,
wherein the rounding plan includes a rounding route of the mobile radiography apparatus. 3. The rounding imaging management apparatus according to claim 2,
wherein an individual necessary time taken for each past radiography is registered as the necessary time in the time results data, wherein the second acquisition unit acquires the individual necessary time corresponding to the radiography indicated by the imaging order information, and wherein the rounding plan includes a predicted total necessary time that is calculated on the basis of the individual necessary time and predicted to be taken for the entire rounding imaging. 4. The rounding imaging management apparatus according to claim 3,
wherein the individual necessary time is at least one of an imaging time of the radiography or a movement time of the mobile radiography apparatus, and wherein the time results data is at least one of imaging time results data in which the imaging time is registered or movement time results data in which the movement time is registered. 5. The rounding imaging management apparatus according to claim 3,
wherein the imaging time results data is data in which a time slot and the individual necessary time are registered in association with each other, and the individual necessary time varies according to the time slot, and wherein the creation unit creates a shortest time route where the predicted total necessary time becomes the shortest as the rounding route. 6. The rounding imaging management apparatus according to claim 5,
wherein the imaging order information includes hospital room information of the hospital room of the patient for whom the rounding imaging is to be performed, and wherein the creation unit creates a shortest distance route where a movement distance of the mobile radiography apparatus becomes the shortest on the basis of the hospital room information, and then, corrects the shortest distance route in accordance with the individual necessary time to create the shortest time route. 7. The rounding imaging management apparatus according to claim 5, further comprising:
a third acquisition unit that acquires patient schedule information in which a schedule of treatment for the patient is registered, wherein the creation unit creates the shortest time route with reference to the patient schedule information. 8. The rounding imaging management apparatus according to claim 5, further comprising:
a fourth acquisition unit that acquires assistant schedule information in which a schedule of an assistant who assists the radiography is registered, wherein the creation unit creates the shortest time route with reference to the assistant schedule information. 9. The rounding imaging management apparatus according to claim 5, further comprising:
a fifth acquisition unit that acquires current status information indicating a current status of information that is a source of creation of the rounding plan during the rounding imaging based on the shortest time route; and an updating unit that updates the shortest time route and sets the updated shortest time route in a case where the current status information includes content which changes the individual necessary time, wherein the output controller outputs the updated shortest time route. 10. The rounding imaging management apparatus according to claim 9,
wherein the current status information is at least one of room occupancy status information indicating a room occupancy status in the hospital room of the patient for whom the rounding imaging is to be performed, treatment status information indicating a status of treatment in the hospital room of the patient for whom the rounding imaging is to be performed, availability status information indicating an availability status of an assistant who assists the radiography, or congestion level information indicating a congestion level of a hospital. 11. The rounding imaging management apparatus according to claim 10, further comprising:
a first estimation unit that estimates an absence time of the patient indicated as being absent in the room occupancy status information, wherein the updating unit updates the shortest time route on the basis of the absence time estimated by the first estimation unit. 12. The rounding imaging management apparatus according to claim 10, further comprising:
a second estimation unit that estimates, in a case where the treatment status information indicates that the treatment is performed in the hospital room, a treatment time to be taken for the treatment, wherein the updating unit updates the shortest time route on the basis of the treatment time estimated by the second estimation unit. 13. The rounding imaging management apparatus according to claim 3, comprising:
a reception unit that receives, in a case where an actual total necessary time in a case where the rounding imaging is actually performed in accordance with the rounding plan is delayed by a set time or longer from the predicted total necessary time, delay cause information indicating a cause of the delay of the actual total necessary time; and a recording controller that performs a control for recording the delay cause information in a storage unit. 14. The rounding imaging management apparatus according to claim 1,
wherein the output controller performs a control for outputting a scheduled start time of the radiography based on the rounding plan. 15. A method for operating a rounding imaging management apparatus that manages rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus, comprising:
acquiring imaging order information indicating content of the radiography in the rounding imaging to be performed; acquiring, from time results data in which a necessary time in the rounding imaging performed in the past is registered, the necessary time; creating a rounding plan of the rounding imaging on the basis of the imaging order information and the necessary time; and performing a control for outputting the rounding plan. 16. A non-transitory computer-readable storage medium storing a program for operating rounding imaging management apparatus that manages rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus, the program causing a computer to function as:
a first acquisition unit that acquires imaging order information indicating content of the radiography in the rounding imaging to be performed; a second acquisition unit that acquires, from time results data in which a necessary time in the rounding imaging performed in the past is registered, the necessary time; a creation unit that creates a rounding plan of the rounding imaging on the basis of the imaging order information and the necessary time; and an output controller that performs a control for outputting the rounding plan. 17. Anon-transitory computer-readable storage medium storing a data structure in which a necessary time in rounding imaging performed in the past is registered, in order to manage the rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus. 18. A recording apparatus comprising a recording controller that records a necessary time in rounding imaging performed in the past is stored in a storage unit, in order to manage the rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus.
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338,201
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| 2,917
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A CPU of a rounding imaging management apparatus functions as a first acquisition unit, a second acquisition unit, a creation unit, and an output controller. The first acquisition unit acquires imaging order information indicating content of radiography in the rounding imaging to be performed. The second acquisition unit acquires, from time results data in which a necessary time in the rounding imaging performed in the past is registered, the necessary time. The creation unit creates a rounding plan of the rounding imaging on the basis of the imaging order information and the necessary time. The output controller performs a control for outputting the rounding plan.
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1. A rounding imaging management apparatus that manages rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus, comprising:
a first acquisition unit that acquires imaging order information indicating content of the radiography in the rounding imaging to be performed; a second acquisition unit that acquires, from time results data in which a necessary time in the rounding imaging performed in the past is registered, the necessary time; a creation unit that creates a rounding plan of the rounding imaging on the basis of the imaging order information and the necessary time; and an output controller that performs a control for outputting the rounding plan. 2. The rounding imaging management apparatus according to claim 1,
wherein the rounding plan includes a rounding route of the mobile radiography apparatus. 3. The rounding imaging management apparatus according to claim 2,
wherein an individual necessary time taken for each past radiography is registered as the necessary time in the time results data, wherein the second acquisition unit acquires the individual necessary time corresponding to the radiography indicated by the imaging order information, and wherein the rounding plan includes a predicted total necessary time that is calculated on the basis of the individual necessary time and predicted to be taken for the entire rounding imaging. 4. The rounding imaging management apparatus according to claim 3,
wherein the individual necessary time is at least one of an imaging time of the radiography or a movement time of the mobile radiography apparatus, and wherein the time results data is at least one of imaging time results data in which the imaging time is registered or movement time results data in which the movement time is registered. 5. The rounding imaging management apparatus according to claim 3,
wherein the imaging time results data is data in which a time slot and the individual necessary time are registered in association with each other, and the individual necessary time varies according to the time slot, and wherein the creation unit creates a shortest time route where the predicted total necessary time becomes the shortest as the rounding route. 6. The rounding imaging management apparatus according to claim 5,
wherein the imaging order information includes hospital room information of the hospital room of the patient for whom the rounding imaging is to be performed, and wherein the creation unit creates a shortest distance route where a movement distance of the mobile radiography apparatus becomes the shortest on the basis of the hospital room information, and then, corrects the shortest distance route in accordance with the individual necessary time to create the shortest time route. 7. The rounding imaging management apparatus according to claim 5, further comprising:
a third acquisition unit that acquires patient schedule information in which a schedule of treatment for the patient is registered, wherein the creation unit creates the shortest time route with reference to the patient schedule information. 8. The rounding imaging management apparatus according to claim 5, further comprising:
a fourth acquisition unit that acquires assistant schedule information in which a schedule of an assistant who assists the radiography is registered, wherein the creation unit creates the shortest time route with reference to the assistant schedule information. 9. The rounding imaging management apparatus according to claim 5, further comprising:
a fifth acquisition unit that acquires current status information indicating a current status of information that is a source of creation of the rounding plan during the rounding imaging based on the shortest time route; and an updating unit that updates the shortest time route and sets the updated shortest time route in a case where the current status information includes content which changes the individual necessary time, wherein the output controller outputs the updated shortest time route. 10. The rounding imaging management apparatus according to claim 9,
wherein the current status information is at least one of room occupancy status information indicating a room occupancy status in the hospital room of the patient for whom the rounding imaging is to be performed, treatment status information indicating a status of treatment in the hospital room of the patient for whom the rounding imaging is to be performed, availability status information indicating an availability status of an assistant who assists the radiography, or congestion level information indicating a congestion level of a hospital. 11. The rounding imaging management apparatus according to claim 10, further comprising:
a first estimation unit that estimates an absence time of the patient indicated as being absent in the room occupancy status information, wherein the updating unit updates the shortest time route on the basis of the absence time estimated by the first estimation unit. 12. The rounding imaging management apparatus according to claim 10, further comprising:
a second estimation unit that estimates, in a case where the treatment status information indicates that the treatment is performed in the hospital room, a treatment time to be taken for the treatment, wherein the updating unit updates the shortest time route on the basis of the treatment time estimated by the second estimation unit. 13. The rounding imaging management apparatus according to claim 3, comprising:
a reception unit that receives, in a case where an actual total necessary time in a case where the rounding imaging is actually performed in accordance with the rounding plan is delayed by a set time or longer from the predicted total necessary time, delay cause information indicating a cause of the delay of the actual total necessary time; and a recording controller that performs a control for recording the delay cause information in a storage unit. 14. The rounding imaging management apparatus according to claim 1,
wherein the output controller performs a control for outputting a scheduled start time of the radiography based on the rounding plan. 15. A method for operating a rounding imaging management apparatus that manages rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus, comprising:
acquiring imaging order information indicating content of the radiography in the rounding imaging to be performed; acquiring, from time results data in which a necessary time in the rounding imaging performed in the past is registered, the necessary time; creating a rounding plan of the rounding imaging on the basis of the imaging order information and the necessary time; and performing a control for outputting the rounding plan. 16. A non-transitory computer-readable storage medium storing a program for operating rounding imaging management apparatus that manages rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus, the program causing a computer to function as:
a first acquisition unit that acquires imaging order information indicating content of the radiography in the rounding imaging to be performed; a second acquisition unit that acquires, from time results data in which a necessary time in the rounding imaging performed in the past is registered, the necessary time; a creation unit that creates a rounding plan of the rounding imaging on the basis of the imaging order information and the necessary time; and an output controller that performs a control for outputting the rounding plan. 17. Anon-transitory computer-readable storage medium storing a data structure in which a necessary time in rounding imaging performed in the past is registered, in order to manage the rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus. 18. A recording apparatus comprising a recording controller that records a necessary time in rounding imaging performed in the past is stored in a storage unit, in order to manage the rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus.
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A CPU of a rounding imaging management apparatus functions as a first acquisition unit, a second acquisition unit, a creation unit, and an output controller. The first acquisition unit acquires imaging order information indicating content of radiography in the rounding imaging to be performed. The second acquisition unit acquires, from time results data in which a necessary time in the rounding imaging performed in the past is registered, the necessary time. The creation unit creates a rounding plan of the rounding imaging on the basis of the imaging order information and the necessary time. The output controller performs a control for outputting the rounding plan.1. A rounding imaging management apparatus that manages rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus, comprising:
a first acquisition unit that acquires imaging order information indicating content of the radiography in the rounding imaging to be performed; a second acquisition unit that acquires, from time results data in which a necessary time in the rounding imaging performed in the past is registered, the necessary time; a creation unit that creates a rounding plan of the rounding imaging on the basis of the imaging order information and the necessary time; and an output controller that performs a control for outputting the rounding plan. 2. The rounding imaging management apparatus according to claim 1,
wherein the rounding plan includes a rounding route of the mobile radiography apparatus. 3. The rounding imaging management apparatus according to claim 2,
wherein an individual necessary time taken for each past radiography is registered as the necessary time in the time results data, wherein the second acquisition unit acquires the individual necessary time corresponding to the radiography indicated by the imaging order information, and wherein the rounding plan includes a predicted total necessary time that is calculated on the basis of the individual necessary time and predicted to be taken for the entire rounding imaging. 4. The rounding imaging management apparatus according to claim 3,
wherein the individual necessary time is at least one of an imaging time of the radiography or a movement time of the mobile radiography apparatus, and wherein the time results data is at least one of imaging time results data in which the imaging time is registered or movement time results data in which the movement time is registered. 5. The rounding imaging management apparatus according to claim 3,
wherein the imaging time results data is data in which a time slot and the individual necessary time are registered in association with each other, and the individual necessary time varies according to the time slot, and wherein the creation unit creates a shortest time route where the predicted total necessary time becomes the shortest as the rounding route. 6. The rounding imaging management apparatus according to claim 5,
wherein the imaging order information includes hospital room information of the hospital room of the patient for whom the rounding imaging is to be performed, and wherein the creation unit creates a shortest distance route where a movement distance of the mobile radiography apparatus becomes the shortest on the basis of the hospital room information, and then, corrects the shortest distance route in accordance with the individual necessary time to create the shortest time route. 7. The rounding imaging management apparatus according to claim 5, further comprising:
a third acquisition unit that acquires patient schedule information in which a schedule of treatment for the patient is registered, wherein the creation unit creates the shortest time route with reference to the patient schedule information. 8. The rounding imaging management apparatus according to claim 5, further comprising:
a fourth acquisition unit that acquires assistant schedule information in which a schedule of an assistant who assists the radiography is registered, wherein the creation unit creates the shortest time route with reference to the assistant schedule information. 9. The rounding imaging management apparatus according to claim 5, further comprising:
a fifth acquisition unit that acquires current status information indicating a current status of information that is a source of creation of the rounding plan during the rounding imaging based on the shortest time route; and an updating unit that updates the shortest time route and sets the updated shortest time route in a case where the current status information includes content which changes the individual necessary time, wherein the output controller outputs the updated shortest time route. 10. The rounding imaging management apparatus according to claim 9,
wherein the current status information is at least one of room occupancy status information indicating a room occupancy status in the hospital room of the patient for whom the rounding imaging is to be performed, treatment status information indicating a status of treatment in the hospital room of the patient for whom the rounding imaging is to be performed, availability status information indicating an availability status of an assistant who assists the radiography, or congestion level information indicating a congestion level of a hospital. 11. The rounding imaging management apparatus according to claim 10, further comprising:
a first estimation unit that estimates an absence time of the patient indicated as being absent in the room occupancy status information, wherein the updating unit updates the shortest time route on the basis of the absence time estimated by the first estimation unit. 12. The rounding imaging management apparatus according to claim 10, further comprising:
a second estimation unit that estimates, in a case where the treatment status information indicates that the treatment is performed in the hospital room, a treatment time to be taken for the treatment, wherein the updating unit updates the shortest time route on the basis of the treatment time estimated by the second estimation unit. 13. The rounding imaging management apparatus according to claim 3, comprising:
a reception unit that receives, in a case where an actual total necessary time in a case where the rounding imaging is actually performed in accordance with the rounding plan is delayed by a set time or longer from the predicted total necessary time, delay cause information indicating a cause of the delay of the actual total necessary time; and a recording controller that performs a control for recording the delay cause information in a storage unit. 14. The rounding imaging management apparatus according to claim 1,
wherein the output controller performs a control for outputting a scheduled start time of the radiography based on the rounding plan. 15. A method for operating a rounding imaging management apparatus that manages rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus, comprising:
acquiring imaging order information indicating content of the radiography in the rounding imaging to be performed; acquiring, from time results data in which a necessary time in the rounding imaging performed in the past is registered, the necessary time; creating a rounding plan of the rounding imaging on the basis of the imaging order information and the necessary time; and performing a control for outputting the rounding plan. 16. A non-transitory computer-readable storage medium storing a program for operating rounding imaging management apparatus that manages rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus, the program causing a computer to function as:
a first acquisition unit that acquires imaging order information indicating content of the radiography in the rounding imaging to be performed; a second acquisition unit that acquires, from time results data in which a necessary time in the rounding imaging performed in the past is registered, the necessary time; a creation unit that creates a rounding plan of the rounding imaging on the basis of the imaging order information and the necessary time; and an output controller that performs a control for outputting the rounding plan. 17. Anon-transitory computer-readable storage medium storing a data structure in which a necessary time in rounding imaging performed in the past is registered, in order to manage the rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus. 18. A recording apparatus comprising a recording controller that records a necessary time in rounding imaging performed in the past is stored in a storage unit, in order to manage the rounding imaging for radiographing individual patients while rounding hospital rooms using a mobile radiography apparatus.
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338,202
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| 2,917
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The present disclosure relates generally to therapeutic agents that may be useful as inhibitors of Integrated Stress Response (ISR) pathway.
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1. A compound of formula (I) 2. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (I) is a compound of formula (II) 3. The compound of claim 2, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (II) is a compound of formula (IV) 4. The compound of claim 3, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (IV) is a compound of formula (IV-a) 5. The compound of claim 3, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (IV) is a compound of formula (IV-e) 6. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (I) is a compound of formula (III) 7. The compound of claim 6, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (III) is a compound of formula (VI) 8. The compound of claim 7, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (VI) is a compound of formula (VI-a) 9. The compound of claim 7, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (VI) is a compound of formula (VI-c) 10. The compound of claim 6, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (III) is a compound of formula (VII) 11. The compound of claim 10, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (VII) is a compound of formula (VII-a) 12. The compound of claim 10, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (VII) is a compound of formula (VII-c) 13. A compound selected from the group consisting of a compound of Table 1, or a pharmaceutically acceptable salt thereof. 14. A pharmaceutical composition comprising a compound of claim 1, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier. 15. A method of treating a disease or disorder mediated by an integrated stress response (ISR) pathway in an individual in need thereof comprising administering to the individual a therapeutically effective amount of a compound of claim 1, or a pharmaceutically acceptable salt thereof. 16. The method of claim 15, wherein the disease or disorder is a neurodegenerative disease, an inflammatory disease, an autoimmune disease, a metabolic syndrome, a cancer, a vascular disease, an ocular disease, or a musculoskeletal disease. 17. The method of claim 15, wherein the disease is vanishing white matter disease, childhood ataxia with CNS hypomyelination, intellectual disability syndrome, Alzheimer's disease, prion disease, Creutzfeldt-Jakob disease, Parkinson's disease, amyotrophic lateral sclerosis (ALS) disease, cognitive impairment, frontotemporal dementia (FTD), traumatic brain injury, postoperative cognitive dysfunction (PCD), neuro-otological syndromes, hearing loss, Huntington's disease, stroke, chronic traumatic encephalopathy, spinal cord injury, dementias or cognitive impairment, arthritis, psoriatic arthritis, psoriasis, juvenile idiopathic arthritis, asthma, allergic asthma, bronchial asthma, tuberculosis, chronic airway disorder, cystic fibrosis, glomerulonephritis, membranous nephropathy, sarcoidosis, vasculitis, ichthyosis, transplant rejection, interstitial cystitis, atopic dermatitis or inflammatory bowel disease, Crohn's disease, ulcerative colitis, celiac disease, systemic lupus erythematosus, type 1 diabetes, multiple sclerosis, rheumatoid arthritis, alcoholic liver steatosis, obesity, glucose intolerance, insulin resistance, hyperglycemia, fatty liver, dyslipidemia, hyperlipidemia, type 2 diabetes, pancreatic cancer, breast cancer, kidney cancer, bladder cancer, prostate cancer, testicular cancer, urothelial cancer, endometrial cancer, ovarian cancer, cervical cancer, renal cancer, esophageal cancer, gastrointestinal stromal tumor (GIST), multiple myeloma, cancer of secretory cells, thyroid cancer, gastrointestinal carcinoma, chronic myeloid leukemia, hepatocellular carcinoma, colon cancer, melanoma, malignant glioma, glioblastoma, glioblastoma multiforme, astrocytoma, dysplastic gangliocytoma of the cerebellum, Ewing's sarcoma, rhabdomyosarcoma, ependymoma, medulloblastoma, ductal adenocarcinoma, adenosquamous carcinoma, nephroblastoma, acinar cell carcinoma, lung cancer, non-Hodgkin's lymphoma, Burkitt's lymphoma, chronic lymphocytic leukemia, monoclonal gammopathy of undetermined significance (MGUS), plasmocytoma, lymphoplasmacytic lymphoma, acute lymphoblastic leukemia, Pelizaeus-Merzbacher disease, atherosclerosis, abdominal aortic aneurism, carotid artery disease, deep vein thrombosis, Buerger's disease, chronic venous hypertension, vascular calcification, telangiectasia or lymphoedema, glaucoma, age-related macular degeneration, inflammatory retinal disease, retinal vascular disease, diabetic retinopathy, uveitis, rosacea, Sjogren's syndrome or neovascularization in proliferative retinopathy, hyperhomocysteinemia, skeletal muscle atrophy, myopathy, muscular dystrophy, muscular wasting, sarcopenia, Duchenne muscular dystrophy (DMD), Becker's disease, myotonic dystrophy, X-linked dilated cardiomyopathy, or spinal muscular atrophy (SMA). 18. A method of producing a protein, comprising contacting a eukaryotic cell comprising a nucleic acid encoding the protein with the compound or salt of claim 1. 19. A method of culturing a eukaryotic cell comprising a nucleic acid encoding a protein, comprising contacting the eukaryotic cell with an in vitro culture medium comprising a compound or salt of claim 1. 20. A method of producing a protein, comprising contacting a cell-free protein synthesis (CFPS) system comprising eukaryotic initiation factor 2 (eIF2) and a nucleic acid encoding a protein with the compound or salt of claim 1. 21. An in vitro cell culture medium, comprising the compound or salt of claim 1 and nutrients for cellular growth. 22. A cell-free protein synthesis (CFPS) system comprising eukaryotic initiation factor 2 (eIF2) and a nucleic acid encoding a protein with the compound or salt of claim 1.
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The present disclosure relates generally to therapeutic agents that may be useful as inhibitors of Integrated Stress Response (ISR) pathway.1. A compound of formula (I) 2. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (I) is a compound of formula (II) 3. The compound of claim 2, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (II) is a compound of formula (IV) 4. The compound of claim 3, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (IV) is a compound of formula (IV-a) 5. The compound of claim 3, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (IV) is a compound of formula (IV-e) 6. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (I) is a compound of formula (III) 7. The compound of claim 6, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (III) is a compound of formula (VI) 8. The compound of claim 7, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (VI) is a compound of formula (VI-a) 9. The compound of claim 7, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (VI) is a compound of formula (VI-c) 10. The compound of claim 6, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (III) is a compound of formula (VII) 11. The compound of claim 10, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (VII) is a compound of formula (VII-a) 12. The compound of claim 10, or a pharmaceutically acceptable salt thereof, wherein the compound of formula (VII) is a compound of formula (VII-c) 13. A compound selected from the group consisting of a compound of Table 1, or a pharmaceutically acceptable salt thereof. 14. A pharmaceutical composition comprising a compound of claim 1, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier. 15. A method of treating a disease or disorder mediated by an integrated stress response (ISR) pathway in an individual in need thereof comprising administering to the individual a therapeutically effective amount of a compound of claim 1, or a pharmaceutically acceptable salt thereof. 16. The method of claim 15, wherein the disease or disorder is a neurodegenerative disease, an inflammatory disease, an autoimmune disease, a metabolic syndrome, a cancer, a vascular disease, an ocular disease, or a musculoskeletal disease. 17. The method of claim 15, wherein the disease is vanishing white matter disease, childhood ataxia with CNS hypomyelination, intellectual disability syndrome, Alzheimer's disease, prion disease, Creutzfeldt-Jakob disease, Parkinson's disease, amyotrophic lateral sclerosis (ALS) disease, cognitive impairment, frontotemporal dementia (FTD), traumatic brain injury, postoperative cognitive dysfunction (PCD), neuro-otological syndromes, hearing loss, Huntington's disease, stroke, chronic traumatic encephalopathy, spinal cord injury, dementias or cognitive impairment, arthritis, psoriatic arthritis, psoriasis, juvenile idiopathic arthritis, asthma, allergic asthma, bronchial asthma, tuberculosis, chronic airway disorder, cystic fibrosis, glomerulonephritis, membranous nephropathy, sarcoidosis, vasculitis, ichthyosis, transplant rejection, interstitial cystitis, atopic dermatitis or inflammatory bowel disease, Crohn's disease, ulcerative colitis, celiac disease, systemic lupus erythematosus, type 1 diabetes, multiple sclerosis, rheumatoid arthritis, alcoholic liver steatosis, obesity, glucose intolerance, insulin resistance, hyperglycemia, fatty liver, dyslipidemia, hyperlipidemia, type 2 diabetes, pancreatic cancer, breast cancer, kidney cancer, bladder cancer, prostate cancer, testicular cancer, urothelial cancer, endometrial cancer, ovarian cancer, cervical cancer, renal cancer, esophageal cancer, gastrointestinal stromal tumor (GIST), multiple myeloma, cancer of secretory cells, thyroid cancer, gastrointestinal carcinoma, chronic myeloid leukemia, hepatocellular carcinoma, colon cancer, melanoma, malignant glioma, glioblastoma, glioblastoma multiforme, astrocytoma, dysplastic gangliocytoma of the cerebellum, Ewing's sarcoma, rhabdomyosarcoma, ependymoma, medulloblastoma, ductal adenocarcinoma, adenosquamous carcinoma, nephroblastoma, acinar cell carcinoma, lung cancer, non-Hodgkin's lymphoma, Burkitt's lymphoma, chronic lymphocytic leukemia, monoclonal gammopathy of undetermined significance (MGUS), plasmocytoma, lymphoplasmacytic lymphoma, acute lymphoblastic leukemia, Pelizaeus-Merzbacher disease, atherosclerosis, abdominal aortic aneurism, carotid artery disease, deep vein thrombosis, Buerger's disease, chronic venous hypertension, vascular calcification, telangiectasia or lymphoedema, glaucoma, age-related macular degeneration, inflammatory retinal disease, retinal vascular disease, diabetic retinopathy, uveitis, rosacea, Sjogren's syndrome or neovascularization in proliferative retinopathy, hyperhomocysteinemia, skeletal muscle atrophy, myopathy, muscular dystrophy, muscular wasting, sarcopenia, Duchenne muscular dystrophy (DMD), Becker's disease, myotonic dystrophy, X-linked dilated cardiomyopathy, or spinal muscular atrophy (SMA). 18. A method of producing a protein, comprising contacting a eukaryotic cell comprising a nucleic acid encoding the protein with the compound or salt of claim 1. 19. A method of culturing a eukaryotic cell comprising a nucleic acid encoding a protein, comprising contacting the eukaryotic cell with an in vitro culture medium comprising a compound or salt of claim 1. 20. A method of producing a protein, comprising contacting a cell-free protein synthesis (CFPS) system comprising eukaryotic initiation factor 2 (eIF2) and a nucleic acid encoding a protein with the compound or salt of claim 1. 21. An in vitro cell culture medium, comprising the compound or salt of claim 1 and nutrients for cellular growth. 22. A cell-free protein synthesis (CFPS) system comprising eukaryotic initiation factor 2 (eIF2) and a nucleic acid encoding a protein with the compound or salt of claim 1.
| 2,900
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338,203
| 16,799,810
| 2,917
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,204
| 29,725,223
| 2,924
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,205
| 29,725,217
| 2,924
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,206
| 29,725,242
| 2,914
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,207
| 29,725,224
| 2,914
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,208
| 29,725,266
| 2,914
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,209
| 29,725,261
| 2,914
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,210
| 29,725,229
| 2,913
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,211
| 29,725,221
| 2,913
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,212
| 29,725,222
| 2,913
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,213
| 29,725,214
| 2,921
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,214
| 29,725,259
| 2,921
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,215
| 29,725,267
| 2,921
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,216
| 29,725,281
| 2,921
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,217
| 29,725,284
| 2,921
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,218
| 29,725,282
| 2,921
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,219
| 29,725,270
| 2,921
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,220
| 29,725,227
| 2,921
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,221
| 29,725,275
| 2,921
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,222
| 29,725,256
| 2,921
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,223
| 29,725,244
| 2,913
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,224
| 29,725,271
| 2,914
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,225
| 29,725,262
| 2,917
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,226
| 29,725,251
| 2,914
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,227
| 29,725,248
| 2,914
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,228
| 29,725,273
| 2,914
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,229
| 29,725,237
| 2,914
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,230
| 29,725,260
| 2,914
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,231
| 29,725,240
| 2,914
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,232
| 29,725,246
| 2,914
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,233
| 29,725,288
| 2,922
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,234
| 29,725,212
| 2,922
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,235
| 29,725,301
| 2,922
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,236
| 29,725,311
| 2,917
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,237
| 29,725,303
| 2,917
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,238
| 29,725,304
| 2,917
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,239
| 29,725,305
| 2,917
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,240
| 29,725,268
| 2,917
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,241
| 29,725,312
| 2,917
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,242
| 29,725,323
| 2,917
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,243
| 29,725,234
| 2,917
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,244
| 29,725,258
| 2,917
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,245
| 29,725,285
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,246
| 29,725,297
| 2,925
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,247
| 29,725,255
| 2,925
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,248
| 35,510,186
| 2,914
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,249
| 29,725,329
| 2,915
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,250
| 29,725,226
| 2,915
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,251
| 29,725,238
| 2,915
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,252
| 29,725,228
| 2,915
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,253
| 29,725,239
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,254
| 62,980,453
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,255
| 62,980,457
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,256
| 29,725,313
| 2,916
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,257
| 29,725,330
| 2,916
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,258
| 29,725,299
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,259
| 29,725,290
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,260
| 62,980,464
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,261
| 29,725,314
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,262
| 62,980,459
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,263
| 29,725,309
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,264
| 29,725,250
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,265
| 62,980,451
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,266
| 29,742,155
| 2,911
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,267
| 35,510,590
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,268
| 29,725,320
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,269
| 29,725,298
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,270
| 62,980,441
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
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338,271
| 29,725,316
| 2,917
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,272
| 29,725,331
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,273
| 62,980,445
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,274
| 29,725,269
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,275
| 62,980,478
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
| 2,900
|
338,276
| 29,725,328
| 2,916
|
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.
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1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.1. A set of amplification primers comprising primers for the amplification of at least 11 Y-STR markers wherein the set of primers are configured to provide each set of amplicons of the at least 11 Y-STR markers having a base pair size less than about 220 base pairs. 2. The amplification primer set of claim 1, wherein detection of amplicon base pair size is performed by a mobility-dependent analytical technique. 3. The amplification primer set of claim 2, wherein the mobility-dependent analytical technique is capillary electrophoresis. 4. The amplification primer set of claim 1, wherein detection of the amplicon base pair size is performed by a sequencing technique using no detection of fluorescent dye labels. 5. The amplification primer set of claim 1, further comprising primers for the amplification of more than the 11 Y-STR markers, wherein the primers are configured to provide sets of amplicons of the more than 11 Y-STR markers having a base pair size less than about 410 base pairs. 6. The amplification primer set of claim 1, comprising 25 Y-STR markers. 7. The amplification primer set of claim 1, wherein each set of the amplicons of the at least 11 Y-STR markers is labeled with one of at least 5 dyes. 8. The amplification primer set of claim 7, wherein the at least 5 dyes are fluorescent dyes configured to be spectrally distinct. 9. The amplification primer set of claim 1, wherein at least one set of amplicons of the Y-STR markers comprises a mobility modifier. 10. The amplification primer set of claim 1, wherein the at least 11 Y-STR markers are DYS576, DYS389I, DYS460, DYS458, DYS19, DYS456, DYS390, DYS570, DYS437, DYS393, and DYS439. 11. The amplification primer set of claim 1, further comprising at least 5 Y-STR markers which are rapidly mutating loci. 12. The amplification primer set of claim 11, wherein the at least 5 rapidly mutating Y-STR markers comprise DYF387S1ab, DYS449, DYS570, DYS576, and DYS627. 13. The amplification primer set of claim 12, wherein the at least 5 rapidly mutating Y-STR markers further comprise DYS518. 14. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635, and Y-GATA-H4. 15. The amplification primer set of claim 1, wherein the set of primers for the amplification of at least 11 Y-STR markers is a set of primers for the amplification of DYF387S1ab, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS460, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS481, DYS533, DYS570, DYS576, DYS627, DYS635, DYS643, and Y-GATA-H4. 16. A kit for co-amplifying a set of loci of at least one DNA sample comprising:
a) the primers of claim 1; and b) optionally, a size standard. 17. The kit of claim 16, wherein the size standard comprises an allelic ladder. 18. A method of amplifying alleles of Y-STR markers of a human male comprising the steps of:
contacting a sample suspected to contain a DNA sample of a human male with a set of amplification primers comprising primers for the amplification of the alleles of at least 11 Y-STR markers; and amplifying the sample thereby forming a plurality of sets of amplicons of the at least 11 Y-STR markers wherein each set of the amplicons has a base pair size less than about 220 base pairs. 19. The method of claim 18, further comprising the step of detecting each set of amplicons whereby the alleles of the at least 11 Y-STR markers are identified. 20. The method of claim 18, wherein the detecting is performed by separating the plurality of sets of amplicons using a mobility dependent analysis, wherein the plurality of sets of amplicons are fluorescently labeled. 21-25. (canceled)
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900
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338,280
| 29,725,294
| 2,917
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900
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338,281
| 35,508,909
| 2,915
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900
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338,282
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| 2,912
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900
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338,283
| 29,725,321
| 2,917
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900
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338,284
| 29,725,326
| 2,916
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900
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338,285
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900
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338,286
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| 2,916
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900
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338,287
| 62,980,501
| 2,916
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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338,288
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900
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338,289
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| 2,916
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900
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338,290
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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338,291
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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338,292
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900
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338,293
| 62,980,500
| 2,916
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900
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338,294
| 62,980,499
| 2,916
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900
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338,295
| 62,980,534
| 2,916
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900
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338,296
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900
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338,297
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| 2,916
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
| 2,900
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338,298
| 62,980,483
| 2,916
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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338,299
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.
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1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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In various embodiments, an analytics system determines nucleic acid sequence reads of genetic material in a soil sample from a geographical location. The analytics system determines a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads. The analytics system determines a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location. The analytics system determines a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity. The analytics system determines a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures.1. A system comprising:
a sampling tube for obtaining a soil sample from a geographical location; and one or more processors and a memory, the memory storing computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine nucleic acid sequence reads of genetic material in the soil sample from the geographical location;
determine, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads;
determine, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location;
determine, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity;
determine a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures; and
transmit the measure of the agronomic attribute for display on a client device. 2. The system of claim 1, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 3. The system of claim 1, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 4. The system of claim 1, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 5. The system of claim 1, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 6. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
determine a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 7. The system of claim 1, wherein the memory stores further computer program instructions that when executed by the one or more processors cause the one or more processors to:
filter out at least one metabolic pathway of the plurality of metabolic pathways. 8. A method comprising:
determining nucleic acid sequence reads of genetic material in a soil sample from a geographical location; determining, by processing the nucleic acid sequence reads, a first set of measures of a plurality of gene functions represented in the nucleic acid sequence reads; determining, by processing the plurality of gene functions, a second set of measures of a plurality of metabolic pathways of microorganisms present in soil at the geographical location; determining, by processing the plurality of metabolic pathways, a third set of measures of a plurality of soil health indicators of the soil at the geographical location, the plurality of soil health indicators including a plurality of levels of granularity; and determining a measure of an agronomic attribute of the soil at the geographical location as a function of the first, second, and third sets of measures. 9. The method of claim 8, wherein determining the second set of measures of the plurality of metabolic pathways of microorganisms comprises:
determining a function of measures of constituent genes from the plurality of gene functions. 10. The method of claim 8, wherein determining the third set of measures of the plurality of soil health indicators comprises:
determining a function of the plurality of metabolic pathways corresponding to the nucleic acid sequence reads. 11. The method of claim 8, wherein the plurality of gene functions includes one or more of: nitrogen cycling, phosphorous cycling, carbon cycling, or oxygen availability. 12. The method of claim 8, wherein the agronomic attribute is nitrogen mineralization and the plurality of metabolic pathways includes at least secreted proteases and urea mineralization. 13. The method of claim 8, further comprising:
determining a recommendation for treatment of the soil at the geographical location using at least the measure of the agronomic attribute. 14. The method of claim 8, further comprising:
filtering out at least one metabolic pathway of the plurality of metabolic pathways. 15. The method of claim 8, wherein the plurality of levels of granularity includes a level closer to biological attributes and another level closer to agronomic attributes. 16. A method comprising:
receiving metadata describing a soil sample, the metadata indicating one or more types of crops grown in a geographical location having the soil sample; determining nucleic acid sequence reads of the soil sample; determining, for each nucleic acid sequence read of at least a subset of the nucleic acid sequence reads, functional descriptors of genes represented in the nucleic acid sequence read; determining reference metrics of soil samples from geographical locations in which the one or more types of crops were grown; determining a metric of the soil sample using the functional descriptors and the reference metrics; and transmitting the metric to a client device for display on a user interface. 17. The method of claim 16, wherein determining the metric of the soil sample comprises:
determining a value of a soil health indicator of the soil sample using the functional descriptors; determining a distribution of values of the soil health indicator for the soil samples using the reference metrics; and determining a percentile of the value with respect to the distribution of values. 18. The method of claim 16, wherein determining the functional descriptors comprises:
determining a plurality of functional genes in the soil sample; determining, for each of the plurality of functional genes, a measure of the functional gene in the soil sample; and normalizing the measure to a single copy marker gene abundance. 19. The method of claim 16, wherein determining the nucleic acid sequence reads of the soil sample comprises:
extracting microbial genetic material from the soil sample; generating the nucleic acid sequence reads using the microbial genetic material; and filtering the nucleic acid sequence reads. 20. The method of claim 16, wherein the metadata further indicates global positioning system (GPS) coordinates of the geographical location, at least one attribute describing treatment of the soil sample, or a soil type of the soil sample.
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