Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers

Abstract

Background Whole-genome sequencing (WGS) is a powerful method for revealing the diversity and complexity of the somatic mutation burden of tumours. Here, we investigated the utility of tumour and matched germline WGS for understanding aetiology and treatment opportunities for high-risk individuals with familial breast cancer. Patients and methods We carried out WGS on 78 paired germline and tumour DNA samples from individuals carrying pathogenic variants in BRCA1 ( n = 26) or BRCA2 ( n = 22) or from non-carriers (non- BRCA1/2 ; n = 30). Results Matched germline/tumour WGS and somatic mutational signature analysis revealed patients with unreported, dual pathogenic germline variants in cancer risk genes ( BRCA1 / BRCA2 ; BRCA1 / MUTYH ). The strategy identified that 100% of tumours from BRCA1 carriers and 91% of tumours from BRCA2 carriers exhibited biallelic inactivation of the respective gene, together with somatic mutational signatures suggestive of a functional deficiency in homologous recombination. A set of non- BRCA1/2 tumours also had somatic signatures indicative of BRCA -deficiency, including tumours with BRCA1 promoter methylation, and tumours from carriers of a PALB2 pathogenic germline variant and a BRCA2 variant of uncertain significance. A subset of 13 non- BRCA1/2 tumours from early onset cases were BRCA-proficient, yet displayed complex clustered structural rearrangements associated with the amplification of oncogenes and pathogenic germline variants in TP53 , ATM and CHEK2 . Conclusions Our study highlights the role that WGS of matched germline/tumour DNA and the somatic mutational signatures can play in the discovery of pathogenic germline variants and for providing supporting evidence for variant pathogenicity. WGS-derived signatures were more robust than germline status and other genomic predictors of homologous recombination deficiency, thus impacting the selection of platinum-based or PARP inhibitor therapy. In this first examination of non- BRCA1/2 tumours by WGS, we illustrate the considerable heterogeneity of these tumour genomes and highlight that complex genomic rearrangements may drive tumourigenesis in a subset of cases.

Pan-cancer landscape of homologous recombination deficiency

“…Of all CHORD-HRD patients, 59.7% (126/211) could be explained by biallelic inactivation of either BRCA2 (cluster 1; n=84), BRCA1 (cluster 5; n=31), RAD51C (cluster 2; n=5), or PALB2 (cluster 3; n=6) (Figure 3c). RAD51C and PALB2 were recently linked to HRD as incidental cases using mutational signature based approaches 16,20 and our results now confirm that biallelic inactivation of these two genes results in HRD and is actually a common cause of HRD (albeit to a lesser extent than for BRCA1/2). RAD51C and PALB2 deficient patients shared the BRCA2-type HRD phenotype (absence of duplications) with BRCA2 deficient patients (clusters 1-3; Figure 3c), consistent with previous studies 20,21 .…”

“…RAD51C and PALB2 were recently linked to HRD as incidental cases using mutational signature based approaches 16,20 and our results now confirm that biallelic inactivation of these two genes results in HRD and is actually a common cause of HRD (albeit to a lesser extent than for BRCA1/2). RAD51C and PALB2 deficient patients shared the BRCA2-type HRD phenotype (absence of duplications) with BRCA2 deficient patients (clusters 1-3; Figure 3c), consistent with previous studies 20,21 . On the other hand, only BRCA1 deficient patients (cluster 5) harbored the BRCA1-type HRD phenotype (1-100kb duplications).…”

High-Throughput Functional Evaluation ofBRCA2Variants of Unknown Significance

“…Tumor response to PARP inhibitor therapy has several biomarkers other than BRCA 1/2 inactivation, such as EMSY amplification, Fanconi anemia pathway inactivation, and other HR gene defects 43 . Therefore, it is a good method to evaluate “ BRCA ness” by whole-genome sequencing of tumors based on mutation and rearrangement signatures without the knowledge of the precise causative mutations 44,45 . Nones et al demonstrated that 21 breast cancers from 22 BRCA2 pathogenic mutation carriers (95%) in the study exhibited “ BRCA ness,” whereas only one was BRCA -proficient 45 .…”

“…Therefore, it is a good method to evaluate “ BRCA ness” by whole-genome sequencing of tumors based on mutation and rearrangement signatures without the knowledge of the precise causative mutations 44,45 . Nones et al demonstrated that 21 breast cancers from 22 BRCA2 pathogenic mutation carriers (95%) in the study exhibited “ BRCA ness,” whereas only one was BRCA -proficient 45 . In contrast to the test of BRCAness, the ABCD test is a simple functional method for evaluating BRCA2 variant pathogenicity.…”

Morphologic and Genomic Heterogeneity in the Evolution and Progression of Breast Cancer

“…Most breast cancers have relatively low numbers of SNVs and indels, compared to other cancer types, however, approximately 20% of tumours are associated with defective homologous recombination (HR) double strand break repair (e.g., in particular those arising in BRCA1, BRCA2, PALB2, RAD51C germline mutation carriers), and these exhibit high rates of SNVs and indels. Further, a minority of tumours (<10%) exhibit hypermutator phenotypes, for instance in tumours associated with defective base excision repair (e.g., MUTYH inactivation), mismatch repair (e.g., MSH2, PMS2, MLH1 inactivation) or APOBEC cytidine deaminase activity mutational signatures [8,9,12,14,[17][18][19].…”