Assessment of homologous recombination deficiency and BRCA status in ovarian cancer: Analytical performance and relevance of a decentralized NGS assay for comprehensive genomic profiling.

Abstract

3130 Background: Homologous recombination deficiency (HRD) is a complex biomarker with predictive value in ovarian cancer. Understanding both the causes of HRD, such as pathogenic alterations in homologous recombination repair (HRR) genes, and its consequences, like genomic instability (GI), is crucial for exploring various therapeutic strategies, including the potential use of poly (ADP-ribose) polymerase inhibitors (PARPi). This study evaluates the analytical performance and clinical research relevance of the Oncomine™ Comprehensive Assay Plus (OCA Plus), a distributable next-generation sequencing (NGS) research use assay that offers in a single workflow comprehensive genomic profiling, including HRD evaluation. Methods: The OCA Plus panel was used for comprehensive genomic profiling of a series of 299 ovarian cancer research samples from the PAOLA-1 trial, part of the ARCAGY biorepository. Research samples were analyzed to assess agreement with orthogonal method, specifically for BRCA1 and BRCA2 mutational status, GI status and overall HRD status which combined BRCA1/2 mutational status and GI status. GI status was determined using Genomic Instability Metric (GIM), a quantitative method that characterizes unbalanced copy number changes. Progression-free survival (PFS) was retrospectively studied to determine future clinical relevance. Results: The success rate for DNA sequencing was 100%, starting from a minimal sample input of 20ng of genomic DNA isolated from FFPE tissue blocks. The OCA Plus panel provided a detailed genomic profile in a single workflow, achieving high success rates across all biomarkers tested, including single nucleotide variants/indels and HRD (100%). Overall percent agreement (OPA) for HRD status with orthogonal method was 87%. OPA for BRCA1/2 variants was 98%, while OPA for GI status was 80%. PFS analysis demonstrated a significantly better hazard ratio (HR: 0.51, p < .005) for the cases positive for OCA Plus HRD solution compared to the cases negative for the OCA Plus HRD solution (HR: 0.84, p = 0.43). Conclusions: The OCA Plus solution enables robust and reliable comprehensive genomic profiling with high OPA for BRCA1/2 and HRD status compared to commonly used orthogonal method. Albeit additional studies are due, overall, the reported data suggests its future clinical utility in predicting treatment outcomes in ovarian cancer.