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Cited by 44BRCA gene mutations in cancerGenomics and Rare DiseasesDNA Repair Mechanisms

High-resolution functional mapping of RAD51C by saturation genome editing

Open access
Olvera-León, Rebeca, Zhang, Fang, Offord, Victoria, Zhao, Yajie, Tan, Hong Kee, Gupta, Prashant, Pal, Tuya, Robles-Espinoza, Carla Daniela +12 more·2024·Cell
DOI 10.1016/j.cell.2024.08.039PMC PMC12147941
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Abstract

Pathogenic variants in RAD51C confer an elevated risk of breast and ovarian cancer, while individuals homozygous for specific RAD51C alleles may develop Fanconi anemia. Using saturation genome editing (SGE), we functionally assess 9,188 unique variants, including >99.5% of all possible coding sequence single-nucleotide alterations. By computing changes in variant abundance and Gaussian mixture modeling (GMM), we functionally classify 3,094 variants to be disruptive and use clinical truth sets to reveal an accuracy/concordance of variant classification >99.9%. Cell fitness was the primary assay readout allowing us to observe a phenomenon where specific missense variants exhibit distinct depletion kinetics potentially suggesting that they represent hypomorphic alleles. We further explored our exhaustive functional map, revealing critical residues on the RAD51C structure and resolving variants found in cancer-segregating kindred. Furthermore, through interrogation of UK Biobank and a large multi-center ovarian cancer cohort, we find significant associations between SGE-depleted variants and cancer diagnoses.

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  • Endogenous genome-editing approaches enable the detection of splice-disrupting synonymous and intronic variants, which cannot be readily assessed using cDNA-based library generation methods in MAVE studies.

    “Consequently, these approaches enable the detection of splice-disrupting synonymous and intronic variants, which cannot be readily assessed using cDNA-based library generation methods in MAVE studies (58).”

    From Massively parallel functional genomic assays in endocrinology: from promise to delivery (2026) · cites this paper as [58]

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Authors
Olvera-León, R., Zhang, F., Offord, V., Zhao, Y., Tan, H. K., Gupta, P., Pal, T., Robles-Espinoza, C. D., Arriaga-González, F. G., Matsuyama, L. S. A. S., Delage, E., Dicks, E., Ezquina, S., Rowlands, C. F., Turnbull, C., Pharoah, P., Perry, J. R. B., Jasin, M., Waters, A. J., & Adams, D. J.
Affiliations
  • Wellcome Sanger Institute (GB)
  • Memorial Sloan Kettering Cancer Center (US)
  • University of Cambridge (GB)
  • Vanderbilt-Ingram Cancer Center (US)
  • Institute of Cancer Research (GB)
  • National Health Service (GB)
  • Cedars-Sinai Medical Center (US)
Corresponding author
  • Waters, Andrew J.
  • Adams, David J.
ORCID
Venue
Cell
Publisher
Elsevier BV
Published
2024-10
Volume
187
Issue
20
Pages
5719-5734.e19
ISSN
0092-8674 (ISSN-L)
DOI
10.1016/j.cell.2024.08.039
PMC
PMC12147941
OpenAlex
W4402598144
Cited by
44
References
10
Citations by year
2026: 26 · 2025: 18
FWCI
10.81
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
Funders
  • Wellcome Trust
  • Cancer Research UK
  • National Institutes of Health (R35 CA253174)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › BRCA gene mutations in cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
Keywords
RAD51C, saturation genome editing, pathogenic variant classification, functional mapping, breast cancer, ovarian cancer, Fanconi anemia, hypomorphic allele, missense mutations, cancer risk association, single nucleotide variants
MeSH terms
Gene Editing, Alleles, Breast Neoplasms, DNA-Binding Proteins, Female, Humans, Ovarian Neoplasms, CRISPR-Cas Systems

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