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Germline Testing Data Validate Inferences of Mutational Status for Variants Detected From Tumor-Only Sequencing by Nahed Jalloul; Israel Gomy; Samantha Stokes; Alexander Gusev; Bruce E. Johnson; Neal I. Lindeman; Laura Macconaill; Shridar Ganesan; Judy E. Garber; Hossein Khiabanian is a Medicine article available to read on EtoBox.
What is Germline Testing Data Validate Inferences of Mutational Status for Variants Detected From Tumor-Only Sequencing about?
## PURPOSE Pathogenic germline variants (PGVs) in cancer susceptibility genes are usually identified through germline testing of DNA from blood or saliva: their detection can affect treatment options and potential risk-reduction strategies for patient relatives. PGV can also be identified in tumor sequencing assays, which, when performed without patient-matched normal specimens, render determination of variants' germline or somatic origin critical. ## METHODS Tumor-only sequencing data from 1,608 patients were retrospectively analyzed to infer germline versus somatic status of variants using an information-theoretic, gene-independent approach. Loss of heterozygosity was also determined. Predicted mutational models were compared with clinical germline testing results. Statistical measures were computed to evaluate performance. ## RESULTS Tumor-only sequencing detected 3,988 variants across 70 cancer susceptibility genes for which germline testing data were available. We imputed germline versus somatic status for > 75% of all detected variants, with a sensitivity of 65%, specificity of 88%, and overall accuracy of 86% for pathogenic variants. False omission rate was 3%, signifying mi
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- Author
- Nahed Jalloul; Israel Gomy; Samantha Stokes; Alexander Gusev; Bruce E. Johnson; Neal I. Lindeman; Laura Macconaill; Shridar Ganesan; Judy E. Garber; Hossein Khiabanian
- Publisher
- American Society of Clinical Oncology (ASCO)
- Published
- 2021
- Language
- EN
- Field
- Medicine (Health Sciences)