PMC7447638_01
The patient's pedigree reveals no known family history of hereditary breast, ovarian, or other related cancers.. The proband is the only child to her parents; however, she has three half-siblings through her mother and numerous aunts, uncles, and cousins on both sides of the family. While this suggests that the MEI is de novo in the proband, it is possible that some members of the family may have the variant and have simply not developed cancer due to age-related penetrance. Her grandparents are reported to have died of noncancer-related causes in their 60s and 70s, and it is possible that they died before cancer would have developed. Only sequencing of family members could confirm the de novo status of the BRCA2 MEI; however, samples were not available.
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Fig1
Although there was no reported family history of HBOC-associated cancers (Fig. 1), she met National Comprehensive Cancer Network (NCCN) guidelines for BRCA1/2 testing. Cascade testing was recommended for her at-risk relatives, although it was possible that the MEI was de novo in view of absent cancer family history (Fig. 1).
Molecular detection of the pathogenic MEI.. a An IGV image from the proband. Colored bases indicate a mismatch relative to the reference genome. Strings of colored bases in a row indicate clipped reads at the SVA insertion breakpoint. The sequence on the bottom represents the reference genome. b Clipped reads at the insertion breakpoint were used to infer the structure of the SVA. A consensus sequence was built from both the right- and left-clipped read clusters. The right-clipped consensus represents the 5' sequence of the SVA and demonstrates some 5' truncation relative to an SVA-E sequence. The left-clipped consensus represents the poly-A tail of the sequence. The box labeled "presumed 3' SVA" is not sequenced and not drawn to scale. If there are no additional rearrangements within the SVA sequence, then the nonsequenced portion is likely ~2kb long. A primer designed based on the SINE-R region of known SVA-E elements was used to amplify the 3' insertion breakpoint.
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Fig2
The presence of a 17-bp target site duplication, L1 endonuclease recognition sequence, and poly-A tail together indicate that this SVA insertion occurred by L1-mediated target-primed reverse transcription (Fig. 2).