Integration of functional assay data results provides strong evidence for classification of hundreds of BRCA1 variants of uncertain significance.

Journal Article (Journal Article)

Purpose

BRCA1 pathogenic variant heterozygotes are at a substantially increased risk for breast and ovarian cancer. The widespread uptake of testing has led to a significant increase in the detection of missense variants in BRCA1, the vast majority of which are variants of uncertain clinical significance (VUS), posing a challenge to genetic counseling. Here, we harness a wealth of functional data for thousands of variants to aid in variant classification.

Methods

We have collected, curated, and harmonized functional data for 2701 missense variants representing 24.5% of possible missense variants in BRCA1. Results were harmonized across studies by converting data into binary categorical variables (functional impact versus no functional impact). Using a panel of reference variants we identified a subset of assays with high sensitivity and specificity (≥80%) and apply the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) variant interpretation guidelines to assign evidence criteria for classification.

Results

Integration of data from validated assays provided ACMG/AMP evidence criteria in favor of pathogenicity for 297 variants or against pathogenicity for 2058 representing 96.2% of current VUS functionally assessed. We also explore discordant results and identify limitations in the approach.

Conclusion

High quality functional data are available for BRCA1 missense variants and provide evidence for classification of 2355 VUS according to their pathogenicity.

Full Text

Duke Authors

Cited Authors

  • Lyra, PCM; Nepomuceno, TC; de Souza, MLM; Machado, GF; Veloso, MF; Henriques, TB; Dos Santos, DZ; Ribeiro, IG; Ribeiro, RS; Rangel, LBA; Richardson, M; Iversen, ES; Goldgar, D; Couch, FJ; Carvalho, MA; Monteiro, ANA

Published Date

  • February 2021

Published In

Volume / Issue

  • 23 / 2

Start / End Page

  • 306 - 315

PubMed ID

  • 33087888

Pubmed Central ID

  • PMC7862071

Electronic International Standard Serial Number (EISSN)

  • 1530-0366

International Standard Serial Number (ISSN)

  • 1098-3600

Digital Object Identifier (DOI)

  • 10.1038/s41436-020-00991-0

Language

  • eng