CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer
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Abstract
CIViC is an expert-crowdsourced knowledgebase for Clinical Interpretation of Variants in Cancer describing the therapeutic, prognostic, diagnostic and predisposing relevance of inherited and somatic variants of all types. CIViC is committed to open-source code, open-access content, public application programming interfaces (APIs) and provenance of supporting evidence to allow for the transparent creation of current and accurate variant interpretations for use in cancer precision medicine.
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CancerVar is an AI platform that uses deep learning to predict oncogenicity of somatic variants using functional and clinical features and may provide a robust alternative to manually curated databases such as CiVIC and OncoKB.
“CancerVar (131) is an AI platform that uses a deep learning framework to predict the oncogenicity of somatic variants using both functional and clinical features and may provide a robust alternative to manually curated databases, such as CiVIC (132) and OncoKB ( 133).”
From Artificial Intelligence in Oncology: Current Landscape, Challenges, and Future Directions (2024) · cites this paper as [132]
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- Authors
- Griffith, M., Spies, N. C., Krysiak, K., McMichael, J. F., Coffman, A. C., Danos, A. M., Ainscough, B. J., Ramirez, C. A., Rieke, D. T., Kujan, L., Barnell, E. K., Wagner, A. H., Skidmore, Z. L., Wollam, A., Liu, C. J., Jones, M. R., Bilski, R. L., Lesurf, R., Feng, Y.-Y., Shah, N. M., Bonakdar, M., Trani, L., Matlock, M., Ramu, A., Campbell, K. M., Spies, G. C., Graubert, A. P., Gangavarapu, K., Eldred, J. M., Larson, D. E., Walker, J. R., Good, B. M., Wu, C., Su, A. I., Dienstmann, R., Margolin, A. A., Tamborero, D., Lopez-Bigas, N., Jones, S. J. M., Bose, R., Spencer, D. H., Wartman, L. D., Wilson, R. K., Mardis, E. R., & Griffith, O. L.
- Affiliations
- Washington University in St. Louis (US)
- Charité – Universitätsmedizin Berlin (DE)
- BC Cancer Agency (CA)
- Scripps Research Institute (US)
- Vall d'Hebron Institute of Oncology (ES)
- Oregon Health & Science University (US)
- Institute for Research in Biomedicine (ES)
- Corresponding author
- Griffith, Malachi
- Griffith, Obi L
- ORCID
- Griffith, Malachi
- Spies, Nicholas C
- Krysiak, Kilannin
- McMichael, Joshua F
- Coffman, Adam C
- Danos, Arpad M
- Ainscough, Benjamin J
- Ramirez, Cody A
- Rieke, Damian T
- Kujan, Lynzey
- Barnell, Erica K
- Wagner, Alex H
- Skidmore, Zachary L
- Wollam, Amber
- Liu, Connor J
- Jones, Martin R
- Lesurf, Robert
- Shah, Nakul M
- Bonakdar, Melika
- Trani, Lee
- Matlock, Matthew
- Ramu, Avinash
- Campbell, Katie M
- Graubert, Aaron P
- Gangavarapu, Karthik
- Larson, David E
- Walker, Jason R
- Good, Benjamin M
- Wu, Chunlei
- Su, Andrew I
- Dienstmann, Rodrigo
- Tamborero, David
- Jones, Steven J M
- Bose, Ron
- Spencer, David H
- Wartman, Lukas D
- Wilson, Richard K
- Mardis, Elaine R
- Griffith, Obi L
- Venue
- Nature Genetics
- Published
- 2017-01-31
- Volume
- 49
- Issue
- 2
- Pages
- 170-174
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC5367263
- OpenAlex
- W2583911935
- Cited by
- 628
- References
- 23
- Citations by year
- 2026: 60 · 2025: 48 · 2024: 59 · 2023: 59 · 2022: 83 · 2021: 78 · 2020: 73 · 2019: 71 · 2018: 61 · 2017: 35 · 2016: 1
- FWCI
- 43.82
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature Genetics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion, cc-by)
- PubMed Central (acceptedVersion, cc-by)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion, cc-by)
- Funders
- Institute for Research in Biomedicine
- Centres de Recerca de Catalunya
- Bundesministerium für Bildung und Forschung (031L0023B, 031L0030E)
- Generalitat de Catalunya
- Ministerio de Economía y Competitividad (SAF2015-74072, SAF2015-74072-JIN)
- National Institutes of Health
- National Human Genome Research Institute (U54HG003079, R00HG007940, K99HG007940)
- National Cancer Institute (K08CA166229, F32CA206247, K22CA188163, U01CA209936, T32CA113275)
- National Institute of General Medical Sciences (R25GM103757, R01GM089820)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › BRCA gene mutations in cancer
- Keywords
- civics, variant interpretation, cancer, crowdsourcing, knowledge base, somatic mutations, inherited mutations, cancer susceptibility, precision medicine, evidence provenance
- MeSH terms
- Humans, Mutation, Neoplasms, Genetic Variation, Knowledge Bases, Crowdsourcing
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