Analytical performance of a next-generation sequencing (NGS) assay kit for assessing homologous recombination deficiency (HRD) from solid tumor samples

HRD status is predictive of response to PARP inhibitors (PARPi) in ovarian cancer. Developing reliable methods to assess HRD status is important to enable genomic profiling of tumor types with PARPi indications. Here we describe the analytical performance of the TruSight™ Oncology 500 HRD (TSO 500 HRD) research assay, an in-development NGS kit for assessing HRD using DNA from solid tumor samples. The TSO 500 HRD assay was developed by adding an HRD probe pool targeting genome-wide single nucleotide polymorphisms (SNPs) to the TruSight Oncology 500 (TSO 500) assay to enable Genomic Instability Score (GIS) assessment. For each sample, the DNA library was split into two hybridization reactions, one with TSO 500 probes and the other with HRD probes. Both libraries were pooled for sequencing with 8 samples per NextSeq™ 550 run. The GIS algorithm was licensed from Myriad, re-implemented as part of the DRAGEN Bio-IT software suite and integrated into the TSO 500 analysis workflow. Forty nanograms of DNA extracted from formalin-fixed, paraffin-embedded (FFPE) samples was used as assay input. Samples were also tested with a reference assay as the orthogonal test. Testing of serial dilutions of 8 ovarian cancer samples showed the limit of detection for small variant calling in BRCA1/2 genes is at 5-10% variant allele frequency (VAF), for large rearrangement variant calling in BRCA1/2 genes is at 30-50% VAF, and for GIS is at 30%-40% tumor content. The false positive rate for GIS status and BRCA variants is 0%. Testing of ovarian cancer samples and control samples with multiple operators, reagent lots, and library preparation start days showed >95% concordance in BRCA variant calling and GIS status. The GIS scores were highly concordant with the reference method assay (R = 0.98). The results were robust on both NextSeq 550 and NovaSeq™ 6000 with SP flowcells. The TSO 500 HRD assay demonstrated high analytical sensitivity and specificity in detecting BRCA variants and GIS status for HRD status assessment in ovarian cancer samples. TSO 500 HRD enables high resolution comprehensive genomic profiling alongside HRD assessment to maximize biomarker detection from limited amount of sample.