Identification and Characterization of Germline Mutations in Indian Women with Cancer: A Tertiary Center Next-Generation Sequencing Study

Abstract Hereditary cancer syndromes account for 5 to 10% of all malignancies, with BRCA1/2 and mismatch repair (MMR) genes playing crucial roles in breast, ovarian, and endometrial cancers. However, the prevalence and spectrum of germline mutations in Indian women remain inadequately characterized. The aim of the study was to determine the proportion of patients harboring pathogenic or likely pathogenic (P/LP) variants and compare the mutation frequencies across cancer subtypes to help provide evidence for genetic counseling, cascade screening, and development of population-specific variant annotation resources to enhance precision oncology in India. We prospectively enrolled 244 histopathologically confirmed cancer patients (193 women and 51 men) meeting National Comprehensive Cancer Network criteria for germline testing (August 2022–June 2025). Genomic DNA from peripheral blood underwent targeted enrichment using the GALEAS HereditaryPlus 146-gene panel and next-generation sequencing on an Illumina NextSeq 2000 platform (mean depth ∼500×). Variants were bioinformatically processed, aligned to the GRCh38 reference genome, and classified according to the guidelines of the American College of Medical Genetics and Genomics. P/LP variants were identified in 55/193 women (28.5%) and 6/51 men (11.8%). Among women, the highest mutation rates were observed in endometrial (30.0%), ovarian (28.6%), and breast (28.0%) cancers. BRCA1 (10.9%) and BRCA2 (6.7%) mutations predominated, followed by MMR genes (MLH1, MSH2, MSH6; cumulative 4.7%). Triple-negative breast cancer exhibited the highest mutation burden (35.1%, p < 0.01). Variants of uncertain significance were detected in 8.8% of women (17/193), highlighting the need for population-specific annotation resources. More than one-quarter of Indian women with major gynecological malignancies harbor actionable germline variants. Our findings underscore the importance of routine multigene panel testing, systematic cascade screening in at-risk relatives, and the development of India-specific variant databases to facilitate precision oncology.