Structural variants at theBRCA1/2loci are a common source of homologous repair deficiency in high grade serous ovarian carcinoma

Abstract

Around half of high grade serous ovarian carcinomas (HGSOC) show homologous recombination repair deficiency (HRD), often caused by germline or somatic single nucleotide variant (SNV) mutations or small indels disrupting BRCA1/2. We have uniformly processed the largest collection of whole genome sequencing (WGS) data from HGSOC samples to date (N=205), comprehensively characterising the somatic mutational landscape, and expression at the BRCA1/2 loci. We discover that large structural variants (SV) are a frequent but unappreciated source of BRCA1/2 disruption in these tumours. Somatic structural variation at these loci is dominated by multi-megabase deletions that span the entirety of BRCA1 (median = 4.9Mb) or BRCA2 (median = 6.2Mb), independently affecting a substantial proportion of patients (16%) in addition to those affected by damaging germline or somatic short variants, within the BRCA1/2 coding sequences (24%). In common with previous studies, we show that the presence of damaging somatic SNVs or short indels in BRCA1 (OR=10, 95% CI 1.8-103, p=0.002, adj p=0.027 and BRCA2 (OR=17, 95% CI 2.1-816), p=0.002, adj.p=0.021) was found to influence HRD. For the first time we also study the compound effect of SV and SNV or short indel mutations at both loci, demonstrating that SVs often contribute to compound deficiencies involving SNVs or indels, with large somatic deletions contributing to these compound deficiencies in 15/205 (7%) of samples. Notably the strongest risk of , p=6.6x10 -3 , adj P=8.5x10 -3 ) is generated by combined large deletions at BRCA1 and BRCA2 in the absence of SNVs or indels, affecting 3% of patients. Overall, we show that HRD is a complex phenotype in HGSOC tumours, affected by the patterns of shorter variants such as SNVs and indels, SVs, methylation and expression seen at multiple loci, and we construct a successful (ROC AUC = 0.75) predictive model of HRD using such variables. In addition, HRD impacts patient survival when conferred by mechanisms other than through the well-understood short variants at BRCA1/2, currently exploited in the clinic. These results alter our understanding of the mutational landscape at the BRCA1/2 loci in highly rearranged tumours, and increase the number of patients predicted to benefit from therapies exploiting HRD in tumours such as PARP inhibition. MainHomologous recombination repair deficiency (HRD) is identifiable in many cancers and is particularly prominent in high grade serous ovarian cancer (HGSOC) 1 , affecting around 50% of tumours 2 and leaving detectable mutational spectra across the tumour genome 3 . The mutational landscape of HGSOC is dominated by extensive genomic copy number changes and structural rearrangement driven by chromosome instability and defective DNA repair, rather than the patterns of recurrent point mutation in tumour suppressor and oncogenes often observed in other solid tumours 4,5 .Germline variants disrupting the coding sequence of BRCA1 and BRCA2 are the most common types of HRD-associated defect, occurring in 8% and 6% of ...

The Genomic Landscape of Early-Stage Ovarian High-Grade Serous Carcinoma

“…If sWGS is to be developed for use in clinical trials, it will be imperative to establish robust criteria for sequencing depth, especially in low cellularity samples or small core biopsies. We also did not perform whole exome sequencing or deep WGS, so are unable to comment upon small variants (SNV, indel) beyond our targeted panel nor on larger scale rearrangements (12,41).…”

Unravelling the tumour genome: The evolutionary and clinical impacts of structural variants in tumourigenesis

“…(B) Diagnosis: the stratification of low‐grade gliomas (isocitrate dehydrogenase [IDH] mutant gliomas) has recently been updated by the WHO to include those with or without concurrent 1p and 19q co‐deletion [161]. (C) Treatment targets: tumours with large deletions of both BRCA1 and BRCA2 loci form a subset of HR‐deficient tumours that are exquisitely sensitive to PARP inhibitors [154,155,162]. (D) Treatment response: Mansfield et al [157,158] demonstrated that malignant mesothelioma harbours neoantigens that are generated by complex SVs, and that their generation was associated with the clonal expansion of T cells, indicating that complex SV burden can be used to predict response to immune checkpoint inhibitors.…”

“…Lastly, SVs do not always promote tumour development, and in fact can be deleterious to the tumour. For example, deletions of BRCA1/2 leads to DNA damage repair deficiencies in certain tumours [155,156], and tumours with a large fraction of complex SVs generate vast amounts of neoantigens that may confer susceptibility to immune therapies [157,158].…”

“…BRCA1/2 loss consists of a pathogenic SNV/indel in BRCA1/2 in either the germline or somatic DNA followed by loss of the other allele via copy number neutral loss of heterozygosity or deletion [154,162]. However, recent evidence has emerged from WGS that indicates that tumours with large heterozygous deletions spanning the length of both BRCA1 and BRCA2, in the absence of SNVs/indels, are also more likely to be HR-deficient and may also benefit from PARP inhibitors [155] (Figure 3C). This is an exciting exemplar, where the clinical impact of a known therapeutic target may be extended to a greater number of patients when we comprehensively account for the full structural complexity of tumour genomes.…”

Multiomic Characterization of High-Grade Serous Ovarian Carcinoma Enables High-Resolution Patient Stratification

“…At the gene sequence level, the identification of mutational disruption in BRCA1 and BRCA2 (BRCA1/2m) has ultimately paved the way for the integration of poly-(ADP-ribose) polymerase (PARP) inhibitor use into routine care for some patients (8)(9)(10). Indeed, there continues to be an intense research effort surrounding mechanisms and implications of homologous recombination DNA repair (HRR) disruption beyond BRCA1/2m (11); these include mutation of non-BRCA1/2 HRR genes (12), large-scale genomic variants disrupting BRCA1/2 (13), epigenetic inactivation of HRR players such as BRCA1 and RAD51C (5,14), and overexpression of the BRCA2 regulator EMSY (15,16).…”