Evaluation of quantitative polymerase chain reaction for detecting BRCA1 or BRCA2 copy number loss in high-grade serous ovarian cancer

Abstract Copy number loss (CNL) of tumour suppressors genes, such as BRCA1/2, are frequent but under-researched tumour driver events. Accurate identification of BRCA1/2 CNL has potential therapeutic implications, particularly in high grade serous tubo-ovarian carcinoma (HGSOC), and cost-effective detection methods are desirable. This study assessed quantitative PCR (qPCR) as a method of BRCA1/2 CNL detection in HGSOC, in two patient cohorts (cohort 1 n = 355, cohort 2 n = 86) and a cell line panel (n = 10) using sequencing-based copy number (CN) assessment as a comparator (panel-based sequencing in cohort 1; whole genome sequencing [WGS] in cohort 2 and the cell line panel). The qPCR sensitivity for detecting BRCA1/2 CNL in both clinical cohorts was poor (BRCA1; 0-11.5%, BRCA2; 10-36.8%). There was frequent co-occurrence of BRCA1 and BRCA2 CNL by qPCR (cohort 1; OR 71.8), which was not mirrored in matched sequencing data. There was a significantly higher CN value for the reference gene RPPH1 in cases with qPCR-identified BRCA1/2 co-loss (cohort 1; RPPH1 median CN 5.2 ± 4.8 versus 2.5 ± 1.3, p