Case Review: Whole-Exome Sequencing Analyses Identify Carriers of a Known Likely Pathogenic Intronic BRCA1 Variant in Ovarian Cancer Cases Clinically Negative for Pathogenic BRCA1 and BRCA2 Variants

Abstract

Background: Detecting pathogenic intronic variants resulting in aberrant splicing remains a challenge in routine genetic testing. We describe germline whole-exome sequencing (WES) analyses and apply in silico predictive tools of familial ovarian cancer (OC) cases reported clinically negative for pathogenic BRCA1 and BRCA2 variants. Methods: WES data from 27 familial OC cases reported clinically negative for pathogenic BRCA1 and BRCA2 variants and 53 sporadic early-onset OC cases were analyzed for pathogenic variants in BRCA1 or BRCA2. WES data from carriers of pathogenic BRCA1 or BRCA2 variants were analyzed for pathogenic variants in 10 other OC predisposing genes. Loss of heterozygosity analysis was performed on tumor DNA from variant carriers. Results: BRCA1 c.5407-25T>A intronic variant, identified in two affected sisters and one sporadic OC case, is predicted to create a new splice effecting transcription of BRCA1. WES data from BRCA1 c.5407-25T>A carriers showed no evidence of pathogenic variants in other OC predisposing genes. Sequencing the tumor DNA from the variant carrier showed complete loss of the wild-type allele. Conclusions: The findings support BRCA1 c.5407-25T>A as a likely pathogenic variant and highlight the importance of investigating intronic sequences as causal variants in OC families where the involvement of BRCA1 is highly suggestive.

Genetic analyses of DNA repair pathway associated genes implicate new candidate cancer predisposing genes in ancestrally defined ovarian cancer cases

“…For the discovery of new candidate OC risk variants (study phase I; Figure 1A ), WES data from peripheral blood lymphocytes (PBL) DNA was available from 15 OC cases from 13 families, each family having at least two first-, second- or third-degree relatives with OC. These cases were confirmed negative for PVs in the known OC risk genes: BRCA1 , BRCA2, BRIP1, RAD51C or RAD51D as previously reported ( 47 , 43 ). This group includes three index cases harbouring a LPV in FANCI c.1813C>T; p.Leu605Phe ( 24 ).…”

“…The majority of FC cancer cases self-reported FC ancestry of Quebec as described previously ( 24 , 40 , 41 , 43 , 47 , 50 – 56 ). FC controls from Université de Sherbrooke-The Genetics of Glucose Regulation in Gestation and Growth (Gen3G) ( 57 ) and McGill University-Montreal Neurological Institute (MNI) ( 58 ) biobanks self-reported FC ancestry as described previously ( 43 ).…”

“…The cancer cases and controls not selected for being of FC ancestry of Quebec, mainly of European ancestry are referred to as non-FC groups in this study, were available from different resources. Genetic analyses to determine the spectrum and prevalence of candidate variants in genes that were identified in the study phase I were performed (study phase IV; Figure 1D ) on available genetic data derived from PBL DNA from three independent groups with OC: 9 OC cases from 7 families with at least two close relatives with OC (MIX familial OC cases) ( 47 ); 516 OC familial or sporadic cases from the Australian population (AUS OC cases) ( 17 ) and 412 OC cases as part of The Cancer Genome Atlas (TCGA) Pan-Cancer Atlas project (not selected for ethnicity) ( 60 ) and cancer-free controls as part of the Genome Aggregation Database (gnomAD) v2.1.1. ( 61 ).…”

“…For phase I of the study ( Figure 1A ), WES data was available from PBL DNA from 15 OC index cases from 13 cancer families that had at least one first-, second- or third-degree relative from the same familial branch with OC, and were confirmed being negative for PVs in BRCA1 , BRCA2, BRIP1, RAD51C or RAD51D by WES analyses ( 43 , 47 ). WES had been subjected to a customized bioinformatics pipeline for germline variant calling at the McGill Genome Center as previously reported by our group ( 24 , 43 ).…”

“…We recently reported that not all remaining BRCA1 and BRCA2 negative families with at least two close relatives with OC from the FC population of Quebec by WES analysis were due to PVs in RAD51C , RAD51D or BRIP1 approximating that 40% of such cases are unaccounted for by known or emerging OC predisposing genes ( 33 , 43 , 47 ). Also, we reported that likely pathogenic variants (LPV) in FANCI , a proposed new OC predisposing gene from the Fanconi anemia (FA) pathway, were rarely implicated in familial and sporadic OC cases in this population ( 24 ).…”