Clinical Implementation of Matched Tumor/Germline Sequencing Improves Accuracy of Tumor Genomic Profiling and Therapeutic Recommendations.

Genomic profiling of cancers informs diagnostic and prognostic classification and aids in selection of targeted therapeutics. Targeted, next-generation sequencing of cancer-specific genes is clinically feasible and enables comprehensive somatic reporting; without a matched germline specimen, germline alterations can confound analyses of the somatic profile and create uncertainty in interpretation. We report the validation and implementation of optional matched tumor/germline sequencing in our precision cancer medicine program. Sixty-three cases were selected for technical validation. DNA was analyzed using OncoPanel, a hybrid capture-based sequencing assay of 461 cancer genes. Three analytical pipelines were implemented: tumor-only, matched tumor/germline, and germline-only. For matched tumor/germline, we "rescued" germline alterations in 19 genes with actionable/therapeutic implications. We retrospectively analyzed the first 1600 matched cases to determine the potential clinical utility of this approach. Limit of detection for point mutations/indels was 3% allele fraction; reproducibility was >98%. Matched tumor/germline concordance across 938 somatic calls was 100%. The average TMB was ∼4 mutations/Mb lower than tumor-only sequencing. TMB-high patients were accurately reclassified as TMB-low in 14% of cases. 25% of validation cases (14% post-launch) had a pathogenic or likely pathogenic germline variant conferring cancer susceptibility; 14% of validation cases (7% post-launch) harbored a germline variant of therapeutic significance. Matched tumor/germline sequencing is more accurate than tumor-only sequencing, while still encompassing all genomic findings that inform targeted therapy selection.