Whole-genome sequencing of >8,000 TCGA samples reveals diverse and atypical spectra of homologous recombination deficiency in primary human cancers

Mutations not only drive carcinogenesis but also record the evolutionary history of cancer. Homologous recombination deficiency (HRD), a defect in high-fidelity DNA double-strand break repair, produces characteristic mutational footprints that define an HRD phenotype. HRD has major clinical relevance as a predictor of response to DNA-damaging agents and targeted therapies, yet current HRD assays were developed primarily in breast and ovarian cancers, and their applicability to other tumor types remains unclear. We conducted a pan-cancer whole-genome analysis of >8,000 primary tumors from The Cancer Genome Atlas (TCGA), spanning ~30 cancer types, including ~900 breast and 300 ovarian cancers. We developed HRDecide, an HRDetect-derived framework that uses comprehensively annotated germline and somatic mutations in homologous recombination (HR) pathway genes, including structural variants and non-canonical splice alterations informed by recent advances in variant-effect prediction, to refine HRD identification across cancer types. Applying HRDecide to TCGA whole-genome sequencing data, we identified HRD-positive tumors and delineated their mutational signatures. HRD-associated features were broadly shared across cancers, extending beyond breast and ovarian tumors to include tumor types such as prostate, pancreatic, gastric, and hepatocellular carcinomas. These signatures encompassed canonical short deletions with microhomology as well as cancer type-specific patterns across substitution, indel, and structural variation profiles. Notably, we also characterized atypical HRD-like phenotypes that showed only a subset of components of the classical HRD signatures. The spectrum of inactivated HR pathway genes, and the predominant modes of disruption, point mutation, structural variation, and allelic loss, varied substantially by cancer type. The scale of this cohort enabled robust associations between HRD phenotypes and pathogenic mutations in HR pathway genes, such as ATM , CHEK2 , and RAD51B , often truncated by structural variations and LINE-1 retrotranspositions, extending beyond the classical BRCA1/2, PALB2, and RAD51C events reported in PCAWG and Hartwig datasets. In summary, this pan-cancer study provides a comprehensive whole-genome landscape of HRD in primary tumors, revealing tissue-specific modes of repair failure and expanding the HRD spectrum beyond the BRCA-centered paradigm. These findings establish a reference framework for tissue-agnostic HRD biomarker development and therapeutic stratification across cancer types.