Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification

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.

High-Throughput Functional Evaluation of BRCA2 Variants of Unknown Significance

“…Initially, a total of 107 BRCA2 variants were selected from a curated database, the BRCA Exchange 24 ( Supplementary Table 1 ). Of these, 32, 10, and 65 variants were classified as benign (Class 1/2), pathogenic (Class 4/5), and VUSs (Class 3), respectively, according to the multifactorial five-tier classification system developed by the International Agency for Research on Cancer (IARC) 10,11,18,25,26 . These BRCA2 variant cDNAs were generated by site-directed mutagenesis and were then subcloned into the piggyBac vector containing unique 10 bp DNA barcode sequences.…”

“…This discrepancy among clinical databases implies potential errors in the interpretation of clinical variants. Moreover, the IARC and ACMG classification methods were designed for detecting high-risk pathogenic variants, and therefore, hypomorphic function variants or moderate cancer risk variants could be classified inappropriately 25 . Hence, we regard the discrepancy between functional and epidemiological evidence as reasonable.…”

Variants of uncertain significance in the era of high-throughput genome sequencing: a lesson from breast and ovary cancers

“…ENIGMA is a wide research-based collaboration with the aim of providing methods to facilitate specifically the classification of the BRCA1 and BRCA2 genes and of other BC susceptibility genes. For this purpose, the consortium provides the criteria for assessing variant significance based on multifactorial likelihood models that include population and clinical evaluations and bioinformatic predictions, and promotes data sharing of large-scale projects with variant annotations [26,42]. Over time, the ENIGMA variant classification data have been collected in the global BRCA Exchange database, together with data from other clinical and population databases (e.g., ClinVar, LOVD, GnomAD), to provide updated and revised reports of variant interpretations [43].…”

Classification of variants of uncertain significance in BRCA1 and BRCA2 using personal and family history of cancer from individuals in a large hereditary cancer multigene panel testing cohort

“…The values derived from theses analyses of in silico prediction are posted on the website 6 and are used as prior probabilities in multifactorial models for classification of VUS by the BRCA1/ 2 expert panel (ENIGMA) and other groups. 7 Because of the efforts of commercial labs, independent research efforts, and in particular the work of the ENIGMA consortium 8,9 over the ten years following the initial study, many VUS have been reclassified as pathogenic or benign with respect to cancer risk. However, we note that due to the increased volume of genetic testing, the absolute numbers of individuals receiving an inconclusive BRCA1/BRCA2 test result are still quite large, with roughly equal numbers of VUS (7360) and pathogenic/likely pathogenic variants (6968) in BRCA1/BRCA2 listed in the National Institutes of Health (NIH) repository ClinVar (https://www.ncbi.nlm.nih.gov/ clinvar; accessed 17 May 2019).…”