Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification
Open Access
- 27 May 2019
- journal article
- research article
- Published by Hindawi Limited in Human Mutation
- Vol. 40 (9), 1557-1578
- https://doi.org/10.1002/humu.23818
Abstract
The multifactorial likelihood analysis method has demonstrated utility for quantitative assessment of variant pathogenicity for multiple cancer syndrome genes. Independent data types currently incorporated in the model for assessing BRCA1 and BRCA2 variants include clinically calibrated prior probability of pathogenicity based on variant location and bioinformatic prediction of variant effect, co‐segregation, family cancer history profile, co‐occurrence with a pathogenic variant in the same gene, breast tumor pathology, and case‐control information. Research and clinical data for multifactorial likelihood analysis were collated for 1,395 BRCA1/2 predominantly intronic and missense variants, enabling classification based on posterior probability of pathogenicity for 734 variants: 447 variants were classified as (likely) benign, and 94 as (likely) pathogenic; and 248 classifications were new or considerably altered relative to ClinVar submissions. Classifications were compared with information not yet included in the likelihood model, and evidence strengths aligned to those recommended for ACMG/AMP classification codes. Altered mRNA splicing or function relative to known nonpathogenic variant controls were moderately to strongly predictive of variant pathogenicity. Variant absence in population datasets provided supporting evidence for variant pathogenicity. These findings have direct relevance for BRCA1 and BRCA2 variant evaluation, and justify the need for gene‐specific calibration of evidence types used for variant classification.Keywords
Funding Information
- Canadian Institutes of Health Research (PSR‐SIIRI‐701)
- Cancer Research UK (C8197/A16565, C5047/A8384, C1281/A12014, C12292/A11174, C1287/A10710, C1287/A10118, C1287/A16563, C5047/A10692, C5047/A15007)
- Generalitat de Catalunya (PERIS_MedPerCan, URDCat, 2017SGR1282, 2017SGR496)
- Royal Society of New Zealand
- Cancer Council Victoria
- Breast Cancer Research Foundation
- Fundación Mutua Madrileña
- Seventh Framework Programme (634935, 223175, 633784)
- Cancer Council South Australia
- Cancer Council Tasmania
- AstraZeneca
- Newcastle University
- National Institute for Health Research (Manchester Biomedical Research centre (IS‐BRC‐1215)
- Instituto de Salud Carlos III (FIS PI15/00355, FIS PI13/01711, CIBERONC, FIS PI16/01218, PI16/00563)
- National Breast Cancer Foundation
- National Health and Medical Research Council (ID1061778, ID1104808)
- Cancer Council NSW
- Deutsche Krebshilfe ((#110837, #70111850)
- Fondazione Pisa (Grant “Clinical characterization of BRCA 1/2 Mis)
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