A comprehensive genomic framework for identifying genes predisposing to homologous recombination repair-deficient breast or ovarian cancer.

Abstract

Background: Patients with clinical characteristics of increased cancer susceptibility without an identified genetic lesion are regularly seen in clinics. Association studies and matched normal/tumour sequencing have advanced the discovery of Cancer Susceptibility Genes (CSGs), with limitations when used independently. We reasoned that combining these strategies alongside mutational signatures and clinical data could improve CSGs identification.

Methods: Using breast and ovarian cancer exome data from The Cancer Genome Atlas (TCGA-BRCA and TCGA-OV), we developed a genomic framework that evaluates exome-wide associations of Germline Pathogenic Variants (GPVs) harbouring second hits with Homologous Recombination Repair Deficiency (HRD) mutational signatures (HRDSig) to identify novel HRD-related CSGs. This is complemented by clinico-genomic analysis evaluating clinical and biological plausibility.

Results: Our framework confirmed significant associations with HRDSig of BRCA1/2 GPVs with second hits in both TCGA cohorts, validating its performance. THBS4 also reached significance but only co-occurred with other HRD-related events in TCGA-BRCA. Borderline significance was also observed for KIF13B and TESPA1, also only in TCGA-BRCA. The clinico-genomics approach further identified KIF13B and TESPA1, as well as RAD51B and other Fanconi Anaemia pathway-related genes, including FANCD2, warranting further validation.

Conclusions: Our approach provides a framework for the identification of candidate HRD-related CSGs through combined statistical and clinico-genomics analyses. It is adaptable to other mutational signatures/cancer types and will be most effective when applied to larger and well-annotated datasets.