Comprehensive germline sequencing and MLPA analysis in breast cancer patients: 4 years of experience from an Indian cancer institute.

Abstract

e12542 Background: This study captures the clinical data and prevalence of the various germline mutations across breast cancer patients in India. It provides a comprehensive understanding of the common germline mutations along with their effect on treatment outcomes. Methods: Between 2021 and 2024, 208 unselected breast cancer patients, irrespective of gender or age, were enrolled for germline testing during treatment. Comprehensive demographic, clinical, pathological, and treatment data were collected. Germline testing utilized a targeted gene sequencing panel covering 145 genes, including promoter regions and clinically significant variants from databases like ClinVar and BRCA Exchange. Deletion/duplication analysis of 30 genes, including BRCA1/2, was performed using digital MLPA. Variants were classified per ACMG guidelines, and descriptive statistics were applied to analyze mutation patterns. Results: Among 208 patients, 114 (54.8%) had mutations, with 30 (14.4%) carrying pathogenic/likely pathogenic (P/LP) mutations. BRCA1/2 mutations constituted 7.2% (15/208) and accounted for 50% of all P/LP mutations. ATM (2.4%), PALB2 (0.5%), and CHEK2 (0.5%) mutations in addition to the BRCA1/2 mutations, represented 73.3% of all P/LP mutations involving the DNA damage repair (DDR) pathway. Notably, 2.4% (5 patients) carried TP53 mutations linked to Li-Fraumeni syndrome, with phenotypic differences noted within families. Co-mutations were observed in 3 patients, such as BRCA1-MLH1 and ATM-CHEK2, warranting further exploration. Median age of the cohort was 48 years. Patients with P/LP mutations had a significantly lower median age (43 years) compared to those with any mutation (48 years; U test, P=0.038). Male patients (2.8%) showed no pathogenic findings, likely due to sample size limitations. MLPA identified pathogenic mutations in 1% of cases, detecting BRCA1/2 mutations missed by NGS. Pathogenic mutations were disproportionately higher in triple-negative breast cancers (43.3%), with 67% of BRCA1/2-positive cases being triple-negative. TNBC patients were significantly more likely to have a pathogenic mutation compared to HR+ and HER2+ subgroups (Chi-square test, P=0.028). ATM mutations were exclusively hormone receptor-positive, with a subset also HER2-positive. Conclusions: Pathogenic germline mutations were detected in 14.4% of patients, with two-third detected in the DDR pathway, predominantly in BRCA1/2 genes. Additional MLPA testing increased BRCA1/2 mutation detection. TNBC showed higher mutation rates, emphasizing the need for genetic profiling in personalized treatment. Younger patients demonstrated higher mutation prevalence, underscoring the importance of early genetic testing. These findings support integrating genetic profiling into clinical practice especially in high-risk subtypes, to improve outcomes.