Loss-of-function pathogenic variants in BRCA1 confer a predisposition to breast and ovarian cancer. Genetic testing for sequence changes in BRCA1 frequently reveals a missense variant for which the impact on cancer risk and on the molecular function of BRCA1 is unknown. Functional BRCA1 is required for the homology-directed repair (HDR) of double-strand DNA breaks, a critical activity for maintaining genome integrity and tumor suppression. Here, we describe a multiplex HDR reporter assay for concurrently measuring the effects of hundreds of variants of BRCA1 for their role in DNA repair. Using this assay, we characterized the effects of 1,056 amino acid substitutions in the first 192 residues of BRCA1. Benchmarking these results against variants with known effects on DNA repair function or on cancer predisposition, we demonstrate accurate discrimination of loss-of-function versus benign missense variants. We anticipate that this assay can be used to functionally characterize BRCA1 missense variants at scale, even before the variants are observed in results from genetic testing.
A Multiplex Homology-Directed DNA Repair Assay Reveals the Impact of More Than 1,000 BRCA1 Missense Substitution Variants on Protein Function.
Lea M. Starita,Muhtadi M. Islam,Tapahsama Banerjee,A. Adamovich,J. Gullingsrud,S. Fields,J. Shendure,J. Parvin
Published 2018 in American Journal of Human Genetics
ABSTRACT
PUBLICATION RECORD
- Publication year
2018
- Venue
American Journal of Human Genetics
- Publication date
2018-10-01
- Fields of study
Biology, Medicine
- Identifiers
- External record
- Source metadata
Semantic Scholar, PubMed
CITATION MAP
EXTRACTION MAP
CLAIMS
CONCEPTS
- benign missense variant
A missense variant class used as the non-pathogenic comparison group in benchmarking.
- brca1
A DNA repair and cancer-susceptibility gene whose first 192 residues were systematically tested for missense substitutions.
- genetic testing
Clinical sequence testing that can reveal BRCA1 variants before their functional impact is known.
- homology-directed repair
A double-strand DNA break repair pathway whose activity was read out by the reporter assay.
Aliases: HDR
- loss-of-function variant
A variant class that reduces or abolishes BRCA1 function in DNA repair.
Aliases: LoF variant
- missense substitution variants
Amino-acid-changing BRCA1 variants analyzed in the assay to assess their functional effects.
Aliases: missense variants, amino acid substitutions
- multiplex hdr reporter assay
A reporter-based experimental platform designed to measure homology-directed repair activity for many BRCA1 variants concurrently.
Aliases: HDR reporter assay
REFERENCES
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