new technologies for obtaining genome sequence data are being combined with novel bioinformatics analyses to characterize disease samples of many types , in the hope of enhancing our fundamental understanding of susceptibility and onset for inherited diseases , of the somatic changes that take place to initiate cancers and cause metastatic disease , and of the identity and allelic spectra of pathogenic and commensal microbes that infect humans . these sequencing - based discoveries will have a major impact on medical practice , including the development of diagnostic and prognostic assays , the identification of altered proteins to which targeted therapies may be developed , the ability to predict onset and severity of disease , and an improved capability to predict our range of responses to pathogenic agents . they will also create large datasets that effectively identify each patient by their sequence information , establishing the potential of linking a patient to a disease and heightening the need to safeguard the privacy of these data through legislation against genetic discrimination . inherited complex diseases have proved the most pervasive yet recalcitrant examples of human disease to reveal their genomic secrets . from a standpoint of statistical significance , studying inherited disease at the genomic level requires large numbers ( ideally thousands ) of cases ( affected ) versus controls ( unaffected ) to uncover initial findings , as well as the replication of any primary discoveries in other case - control cohorts to solidify the association of a given genomic variant(s ) with disease . although genome - wide association studies ( gwas ) have been broadly applied across the spectrum of hypertension , diabetes , autism and other diseases , the identification of disease - associated genes by gwas has so far identified mainly genes of low effect size or within regions of the genome that do not contain annotated genes , hence making it difficult to assign functionality or even putative causality . with the development and publication of several methods that can selectively isolate sequences of interest from a genomic dna sample , there are now high - throughput methods available for variant discovery within genomic regions identified by gwas or by candidate gene approaches . these methods use a variety of solid - phase   or solution - phase   strategies to capture the desired loci , typically isolating dna fragments that represent hundreds to thousands of genes in a single experiment , which are then sequenced using next - generation sequencing technology . downstream variant discovery aligns the sequences obtained to the targeted regions or genes , and then identifies high - quality sequence differences . a secondary level of interpretation can identify those variants encoding a different amino acid or a premature stop codon likely to impact the structure and function of the proteins containing them . this exercise can provide clues about which modified proteins may be contributing to the disease biology . combining the variant information obtained across affected individuals with an analysis of those cellular pathways in which the altered proteins participate can then enable higher - level concepts to emerge about disease biology . all targeted capture methods are somewhat limited by the fact that they rarely yield 100% coverage of the sequence from any targeted region . as such , where coverage gaps exist variants can not be discovered , but this also occurs with polymerase chain reaction ( pcr)-based approaches . by contrast , the combined targeted capture plus next - generation sequencing generates data much faster , is more scalable in terms of genes targeted and the ability to combine patient samples into a single capture experiment , and is cheaper than the conventional approach of pcr and capillary sequencing . moreover , because each next - generation sequence read represents data from a single dna strand , the ability to discover sequence variants is greatly facilitated over that of diploid pcr product sequences ( both alleles represented in the same reaction ) obtained from a capillary read . targeted capture approaches are now being applied to gwas peaks for many inherited disease studies . the resulting data will reveal the spectrum of rare single nucleotide and insertion - deletion variants , and hopefully will shed additional light on the genomic predisposition to the disease of interest . given the operational scale possible for some of these methods ( for example , solution - phase capture can be carried out readily in a 96-well plate format ) and the massively parallel scale of next - generation sequencing throughput , we will soon know whether this predicted efficacy yields the promised rare variant discoveries . however , the limited representation of the human genome on single nucleotide polymorphism ( snp ) arrays will not provide a complete picture of case - specific variation via gwas . rather , as the price of whole - genome resequencing falls , so will the desire to fully characterize the genomes of inherited , disease - affected individuals by whole genome resequencing so that variant discovery is unbiased . in contrast to inherited disease , somatic diseases such as cancer do not typically require large sample numbers to provide significant discovery potential . both targeted capture and whole - genome resequencing are currently being used to study cancers of various types . here , the list of targeted genes typically is derived by a candidate - based approach , which includes known cancer - associated genes from studies of the particular tumor type , and may possibly include genes lying under genomic regions determined to have altered copy number ( amplification or deletion ) . studies to date using pcr and capillary sequencing have essentially revealed that although many hundreds of genes are sequenced , only a handful attain significant levels of mutation across all samples studied . for example , in a recent study of glioblastoma multiforme , the cancer genome atlas consortium reported that of 601 candidate genes sequenced , only 223 revealed a mutation in at least one of the 91 tumor samples studied and only eight genes could be classified as significantly mutated . similarly , when whole - genome resequencing was used to study an acute myeloid leukemia ( aml ) genome and the genome of its matched normal ( skin ) sample , the eight single - nucleotide non - synonymous variants found were in genes that essentially would never have been on a candidate gene list for aml . this early result has made a strong case for whole - genome resequencing as an unbiased approach by which medical research can pursue the genomic basis of cancer . to date , we have been hindered by the cost of whole - genome resequencing , but the falling cost of next - generation sequencing experiments is quickly eliminating this barrier , and hundreds of cancers will likely be sequenced during 2009 . one interesting concept to note is that , using a variety of dna and rna preparatory methods combined with next - generation sequencing , one can produce sequence - based characterizations of tumors that reveal the spectrum of variation across the genome , the ' methylome ' ( that is , cancer - specific changes in dna methylation patterns ) , and the transcriptome ( expression levels of mrna plus other non - coding rnas ) in comparison to non - cancerous matched tissue . this wealth of data , when coupled with clinically relevant information about the cancer ( age of onset , treatment history , outcome , family history / susceptibility , and so on ) , provides the potential to more fully shape our understanding of the disease biology . with similar analyses in hand for many samples of the same cancer type or subtype , a correlated spectrum of affected genes , pathways , treatment options and outcomes , including findings with translational impacts on patient care , will begin to emerge . only by performing many such studies will we begin to understand how individualized each cancer is , and hence shed light on the importance of whole - genome versus targeted analysis of cancers as a diagnostic or prognostic measure . while cancer and inherited diseases are important disorders to study using genomic data , the combination of viral , bacterial and fungal pathogens adversely impacts many more lives worldwide per year . given the difficulty or impossibility of culturing most pathogenic species , the use of next - generation sequencing has greatly enabled their identification . this typically is accomplished by isolating all nucleic acids from a human sample ( such as feces , tooth or skin scrapings ) , sequencing the isolated dna mixture , and then assembling the non - human sequence reads to reconstruct segments of the pathogenic genomes carried in the sample . next , these dna sequences are translated into amino acid sequences to help identify the novel pathogen(s ) and to characterize gene content and other attributes ( such as antibiotic resistance ) . such ' metagenomic ' studies comprise some of the most exciting discovery - based science happening in medical research today . in terms of known pathogens , the exquisite sensitivity of next - generation sequencing is already being applied to disease management . one brilliant example of this is in human immunodeficiency virus ( hiv ) disease management , where newly diagnosed patients ' sera are input to pcrs that target specific viral genome regions , allowing the clinician to assess the mutational status of each viral population as a precursor to developing a patient - specific drug cocktail . in essence , while there are over 20 hiv - specific therapies available , only by sequencing each patient 's viral population can therapies to which viral resistance already exists be avoided . it also remains unclear whether and how healthy individuals interact with their natural commensal bacterial , viral and eukaryotic species ( ' microbiome ' ) , or how changes to the normal prevalence of various species ( or strains ) may influence our relative wellness . the nih roadmap has set up a human microbiome project   and provided funding to begin to address such questions , as well as to dramatically improve the census of sequenced human microbiome species available in public databases . these genomes will provide a tremendously enhanced database for microbiome- and metagenomic - based queries , furthering medical research in the process of answering the question ' who 's there ? ' for different healthy and disease states . cumulatively , the impact of next - generation sequencing on medical research is beginning to gain momentum , and we can already predict a point at which discoveries resulting from the kind of inquiries described in this commentary may overwhelm our abilities to translate them into clinical applications . after all , sequencing data will provide a multitude of clues , but few direct answers . to meet this challenge , functional screening approaches must scale up to high throughput and our characterization and annotation of human genome functional elements must accelerate . we need to find ways to engage colleagues familiar with biochemistry , cell biology , medicine , pharmacology , and other relevant fields to help interpret discoveries from next - generation sequencing studies and to think about the next steps . and , in an era of genomic data accessibility , we need to ensure the privacy of would - be study volunteers so our work proceeds without the delays that will occur if there is a dearth of properly consented samples . aml : acute myeloid leukemia ; gwas : genome - wide association studies ; hiv : human immunodeficiency virus ; pcr : polymerase chain reaction ; snp : single nucleotide polymorphism . the author was a director of the former applera corporation ( now life technologies ) from 2007 until 2008 . i would like to thank my colleagues , rick wilson , tim ley and george weinstock for critical comments and input .
a variety of techniques that specifically target human gene sequences for differential capture from a genomic sample , coupled with next - generation , massively parallel dna sequencing instruments , is rapidly supplanting the combination of polymerase chain reaction and capillary sequencing to discover coding variants in medically relevant samples . 
 these studies are most appropriate for the sample numbers necessary to identify both common and rare single nucleotide variants , as well as small insertion or deletion events , which may cause complex inherited diseases . 
 the same massively parallel sequencers are simultaneously being used for whole - genome resequencing and comprehensive , genome - wide variant discovery in studies of somatic diseases such as cancer . 
 viral and microbial researchers are using next - generation sequences to identify unknown etiologic agents in human diseases , to study the viral and microbial species that occupy surfaces of the human body , and to inform the clinical management of chronic infectious diseases such as human immunodeficiency virus ( hiv ) . 
 taken together , these approaches are dramatically accelerating the pace of human disease research and are already impacting patient care .