Accurately estimating the homologous recombination deficiency based on low-pass whole-genome sequencing and target sequencing.

Abstract

e15077 Background: Homologous recombination deficiency (HRD) is a promising biomarker for poly ADP-ribose polymerase (PARP) inhibitors. In the past, the HRD status was mainly estimated by summing the loss of heterozygosity (LOH), telomeric allelic imbalance (TAI), and large-scale state transition (LST) based on target sequencing. However, the heterozygous loci coverage and probe number are closely correlated to B allele frequency and copy number variations (CNVs). Here we developed a novel method to combine the data from low-pass whole-genome sequencing (WGS) and target sequencing to accurately estimate the genome-wide CNVs and allelic imbalance. Methods: We first performed low-pass WGS and target sequencing on 30 healthy controls, formalin-fixed and paraffin-embedded (FFPE) samples, and matched blood cell samples for 29 patients with breast cancer or ovarian cancer. Two HRD positive samples were diluted to 40%, 30%, 20%, and 10% tumor purity with matched blood cell samples, respectively. Each diluted sample was sequenced 20 times. The baseline for CNVs was built based on the sequencing data of healthy donors. To eliminate the artifacts resulted from the sequencing platform, models for each candidate single nucleotide polymorphism (SNP) in target regions were trained using the data from healthy donors. The mutations of BRCA1/BRCA2 of 29 patients were used to define the threshold of the HRD score. The numbers of LOH, LST, and TAI were evaluated by CNVs and B allele frequency. Results: We defined a cutoff of 42 for the HRD status based on the low-pass WGS and target sequencing data of 29 patients. Specifically, the original HRD scores for two selected HRD positive samples were 68 and 89. The median HRD scores for 40%, 30%, 20%, and 10% tumor purity samples were 69 and 88, 66.5 and 90, 61 and 68, 52 and 34.5, respectively. Conclusions: We developed a novel method for robustly inferring the HRD status using low-pass WGS and target sequencing with a limit of detection of 20%.