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

Overview

abstract

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 generate 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/insertions and deletions was 3% allele fraction; reproducibility was >98%. Matched tumor/germline concordance across 938 somatic calls was 100%. The average tumor mutational burden (TMB) was approximately 4 mutations/Mb lower than tumor-only sequencing. TMB-high patients were accurately reclassified as TMB-low in 14% of cases. A total of 25% of validation cases (14% after launch) had a pathogenic or likely pathogenic germline variant conferring cancer susceptibility; 14% of validation cases (7% after 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.