Abstract / Summary
Abstract Homologous recombination repair (HRR) gene alterations are key drivers in prostate cancer (PC), and HRR positive (HRR+) patients have shown clinical benefit from Poly ADP-ribose Polymerase (PARP) inhibitors. However, detection of HRR gene alterations often relies on large and costly next-generation sequencing (NGS) panels with prolonged turnaround times (TAT). To overcome these challenges, we developed AmoyDx HRD Complete, a targeted NGS assay for HRR gene alterations with a 4-day TAT. Utilizing a novel HANDLE (Halo-shape ANnealing and Defer-Ligation Enrichment)-based approach, this assay detects single nucleotide variants (SNV), insertions and deletions (InDel), and homozygous deletions (HD) across 17 HRR genes. In this study we evaluated the analytical performance of the assay and applied it to characterize the mutational landscape in a cohort of 398 patients with PC. The sensitivity for SNV/InDel detection was 5% mutant allele fraction (MAF) using 30ng DNA input. For HD, a tumor content of 20% enabled gene-level HD detection, while exon-level HD detection required 40% tumor content using 100ng DNA. No false-positive calls were observed across all variant classes, yielding 100% analytical specificity. Among 398 PC patients, 51 (12.8%) were HRR+; including 45 (11.3%) with pathogenic or likely pathogenic HRR gene SNV/InDel alterations, and an additional 6 (1.5%) with HRR HD. Among the 51 HRR+ patients, 15 were BRCA positive (BRCA+) including 2 BRCA HD. HRR/BRCA alterations were enriched in patients with higher Gleason scores (≥ 8) and those with metastatic disease. Compared with Gleason < 8, patients with Gleason ≥ 8 showed higher prevalence (HRR + 17.5% vs 8.2%, Odds Ratio (OR) 2.38, P = 0.00664; BRCA + 6.0% vs 1.0%, OR 6.19, P = 0.0115). Similarly, metastatic disease was associated with higher HRR+/BRCA+ rates than localized disease (HRR + 29.5% vs 10.7%, OR 3.49, P = 0.00139; BRCA + 9.1% vs 2.8%, OR 3.44, P = 0.057, borderline). With its high sensitivity, specificity, and short TAT, the HRD Complete assay offers a robust and reliable approach for detecting HRR alterations in PC patients, and may help guide treatment decisions.