DNA Repair Function Scores for 2172 Variants in the BRCA1 Amino-Terminus.

Area of Science:

• Genomics
• Molecular Biology
• Cancer Genetics

Background:

• Single nucleotide variants (SNVs) are common genomic alterations, often classified as variants of uncertain significance (VUS) with unknown disease risk.
• BRCA1 tumor suppressor protein is crucial in breast and ovarian cancer; pathogenic variants frequently impair its DNA repair function.
• Functional assays are vital for interpreting VUS and providing accurate genetic risk information to patients.

Approach:

• A multiplexed functional assay measuring homology-directed repair (HDR) of DNA double-strand breaks was employed.
• The assay was used to functionally assess 2172 missense variants in BRCA1 residues 2-302.
• An improved analysis pipeline enhanced variant scoring and expanded coverage to new BRCA1 regions.

Key Points:

• The assay demonstrated high accuracy, with 93% sensitivity and 100% specificity in classifying known pathogenic and benign BRCA1 variants.
• Pathogenic BRCA1 variants consistently showed loss of function in the HDR assay.
• Benign BRCA1 variants exhibited normal function in the assay, validating its predictive capability.

Conclusions:

• The functional assay provides a reliable method for classifying the impact of BRCA1 variants.
• These functional classifications serve as critical evidence for clinical geneticists interpreting VUS in BRCA1.
• This resource can improve patient counseling and genetic risk assessment for hereditary breast and ovarian cancer.