Analytical Validation and Clinical Implementation of MedGenome HRD Assay: A Large Comparative Study Against Commercial HRD Assays in Ovarian Cancer

Background: Homologous recombination deficiency (HRD) is an important predictive biomarker for poly (ADP-ribose) polymerase inhibitor (PARPi) therapy in ovarian cancer (OC). However, real-world data on HRD prevalence and assay performance in Indian patients are limited. This study evaluated commercial HRD assays, then developed an in-house HRD assay and characterized HRD and BRCA alterations in a large real-world Indian OC cohort. Methods: This retrospective study included 4,163 formalin-fixed paraffin-embedded (FFPE) OC samples tested between 2021 and 2025. HRD and BRCA status were initially assessed using the AmoyDx HRD Focus Panel (n=1,097) and SOPHiA DDM HRD Solution (n=470). Subsequently, 170 representative samples were used for the development and validation of an in-house HRD assay (MG_HRD), with external concordance assessed using the Myriad myChoice CDx assay in a subset of samples. Following validation, MG_HRD was implemented in routine clinical practice and applied to an independent cohort of 2,596 OC samples. HRD prevalence, BRCA mutation status, and clinicopathological associations were evaluated in all cohorts. Results: Among 4,163 ovarian cancer samples, HRD positivity was observed in 52.4% of cases, and pathogenic/likely pathogenic BRCA1/2 variants were identified in 23.6% of cases. Notably, 28.8% of tumors were BRCA wild-type but HRD-positive. BRCA-mutated tumors demonstrated significantly higher HRD genomic instability scores than BRCA wild-type tumors (p<0.001). HRD positivity was significantly enriched in high grade serous ovarian carcinomas. Remarkably, the BRCA1 c.68_69del (p.Glu23ValfsTer17) founder mutation was detected in 14.2% (97/685) of cases among the pathogenic variants in our study. The MG_HRD assay showed excellent concordance with commercial assays, achieving 97.1% overall agreement, 98.3% negative percent agreement (NPA), and 96.4% positive percent agreement (PPA), with complete concordance observed in the externally evaluated Myriad subset. Conclusions: This is the first Indian study to develop, validate, and implement an in-house HRD assay and evaluate HRD across three testing platforms in a large real-world OC cohort. The high prevalence of BRCA wild-type/HRD-positive tumors highlight the importance of comprehensive HRD testing, whereas the strong performance of MG_HRD supports its use as a reliable and cost-effective alternative for routine clinical practice. Keywords: ovarian cancer; homologous recombination deficiency; genomic instability, BRCA1/2, mutation, high grade serous carcinoma