0
1

Delete article

Deleted articles cannot be recovered.

Draft of this article would be also deleted.

Are you sure you want to delete this article?

Cosmic: a curated database of somatic variants and clinical data for cancer.

Last updated at Posted at 2025-08-06

Cosmic: a curated database of somatic variants and clinical data for cancer.

Z. Sondka, N. B. Dhir, D. Carvalho-Silva, S. Jupe, Madhumita, K. McLaren, M. Starkey, S. Ward, J. Wilding, M. Ahmed, J. Argasinska, D. Beare, M. S. Chawla, S. Duke, I. Fasanella, A. G. Neogi, S. Haller, B. Hetenyi, L. Hodges, A. Holmes, R. Lyne, T. Maurel, S. Nair, H. Pedro, A. Sangrador-Vegas, H. Schuilenburg, Z. Sheard, S. Y. Yong, and J. Teague. Cosmic: a curated database of somatic variants and clinical data for cancer. Nucleic Acids Research, 52:D1210–D1217, 1 2024. ISSN 0305-1048. doi: 10.1093/NAR/GKAD986. URL https://dx.doi.org/10.1093/nar/gkad986.

References

  1. Chang K., Creighton C.J., Davis C., Donehower L., Drummond J., Wheeler D., Ally A., Balasundaram M., Birol I., Butterfield Y.S.N.et al. . The cancer genome atlas pan-cancer analysis project. Nat. Genet. 2013; 45:1113–1120.
  2. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium Pan-cancer analysis of whole genomes. Nature. 2020; 578:82–93.
  3. Pugh T.J., Bell J.L., Bruce J.P., Doherty G.J., Galvin M., Green M.F., Hunter-Zinck H., Kumari P., Lenoue-Newton M.L., Li M.M.et al. . AACR Project GENIE: 100,000 cases and beyond. Cancer Discov. 2022; 12:2044–2057.
  4. Forbes S.A., Beare D., Boutselakis H., Bamford S., Bindal N., Tate J., Cole C.G., Ward S., Dawson E., Ponting L.et al. . COSMIC: somatic cancer genetics at high-resolution. Nucleic Acids Res. 2017; 45:D777–D783.
  5. Tate J.G., Bamford S., Jubb H.C., Sondka Z., Beare D.M., Bindal N., Boutselakis H., Cole C.G., Creatore C., Dawson E.et al. . COSMIC: the catalogue of somatic mutations In cancer. Nucleic Acids Res. 2019; 47:D941–D947.
  6. Bamford S., Dawson E., Forbes S., Clements J., Pettett R., Dogan A., Flanagan A., Teague J., Futreal P.A., Stratton M.R.et al. . The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br. J. Cancer. 2004; 91:355–358.
  7. Sondka Z., Bamford S., Cole C.G., Ward S.A., Dunham I., Forbes S.A. The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers. Nat. Rev. Cancer. 2018; 18:696–705.
  8. Wilkinson M.D., Dumontier M., Aalbersberg I.J., Appleton G., Axton M., Baak A., Blomberg N., Boiten J.-W., da Silva Santos L.B., Bourne P.E.et al. . The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data. 2016; 3:160018.
  9. Hudson T.J., Anderson W., Aretz A., Barker A.D., Bell C., Bernabé R.R., Bhan M.K., Calvo F., Eerola I., Gerhard D.S.et al. . International network of cancer genome projects. Nature. 2010; 464:993–998.
  10. Seal R.L., Braschi B., Gray K., Jones T.E.M., Tweedie S., Haim-Vilmovsky L., Bruford E.A. Genenames.Org: the HGNC resources in 2023. Nucleic Acids Res. 2023; 51:D1003–D1009.
  11. Eilbeck K., Lewis S.E., Mungall C.J., Yandell M., Stein L., Durbin R., Ashburner M. The Sequence ontology: a tool for the unification of genome annotations. Genome Biol. 2005; 6:R44.
  12. den Dunnen J.T., Dalgleish R., Maglott D.R., Hart R.K., Greenblatt M.S., McGowan-Jordan J., Roux A.F., Smith T., Antonarakis S.E., Taschner P.E. HGVS recommendations for the description of sequence variants: 2016 update. Hum. Mutat. 2016; 37:564–569.
  13. Martin F.J., Amode M.R., Aneja A., Austine-Orimoloye O., Azov A.G., Barnes I., Becker A., Bennett R., Berry A., Bhai J.et al. . Ensembl 2023. Nucleic Acids Res. 2023; 51:D933–D941.
  14. Sioutos N., Coronado S.d., Haber M.W., Hartel F.W., Shaiu W.-L., Wright L.W. NCI Thesaurus: a semantic model integrating cancer-related clinical and molecular information. J. Biomed. Inform. 2007; 40:30–43.
  15. Frankish A., Diekhans M., Jungreis I., Lagarde J., Loveland J.E., Mudge J.M., Sisu C., Wright J.C., Armstrong J., Barnes I.et al. . Gencode 2021. Nucleic Acids Res. 2021; 49:D916–D923.
  16. McLaren W., Gil L., Hunt S.E., Riat H.S., Ritchie G.R.S., Thormann A., Flicek P., Cunningham F. The Ensembl variant effect predictor. Genome Biol. 2016; 17:122.
  17. Alexandrov L.B., Kim J., Haradhvala N.J., Huang M.N., Tian Ng A.W., Wu Y., Boot A., Covington K.R., Gordenin D.A., Bergstrom E.N.et al. . The repertoire of mutational signatures in human cancer. Nature. 2020; 578:94–101.
  18. Koh G., Degasperi A., Zou X., Momen S., Nik-Zainal S. Mutational signatures: emerging concepts, caveats and clinical applications. Nat. Rev. Cancer. 2021; 21:619–637.
  19. Islam S.M.A., Díaz-Gay M., Wu Y., Barnes M., Vangara R., Bergstrom E.N., He Y., Vella M., Wang J., Teague J.W.et al. . Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor. Cell Genomics. 2022; 2:https://doi.org/10.1016/j.xgen.2022.100179.
  20. Landrum M.J., Lee J.M., Benson M., Brown G.R., Chao C., Chitipiralla S., Gu B., Hart J., Hoffman D., Jang W.et al. . ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Res. 2018; 46:D1062–D1067.
  21. Karczewski K.J., Francioli L.C., Tiao G., Cummings B.B., Alföldi J., Wang Q., Collins R.L., Laricchia K.M., Ganna A., Birnbaum D.P.et al. . The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020; 581:443–434.
  22. Martincorena I., Raine K.M., Gerstung M., Dawson K.J., Haase K., Van Loo P., Davies H., Stratton M.R., Campbell P.J. Universal patterns of selection in cancer and somatic tissues. Cell. 2017; 171:1029–1041.
  23. Cooper G.M., Stone E.A., Asimenos G., Green E.D., Batzoglou S., Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005; 15:901–913.
  24. Vaser R., Adusumalli S., Leng S.N., Sikic M., Ng P.C. SIFT missense predictions for genomes. Nat. Protoc. 2016; 11:1–9.
  25. Hanahan D. Hallmarks of cancer: new dimensions. Cancer Discov. 2022; 12:31–46.
  26. Hanahan D., Weinberg R.A. The hallmarks of cancer. Cell. 2000; 100:57–70.
  27. Hanahan D., Weinberg R.A. Hallmarks of cancer: the next generation. Cell. 2011; 144:646–674.
  28. Eisenhauer E.A., Therasse P., Bogaerts J., Schwartz L.H., Sargent D., Ford R., Dancey J., Arbuck S., Gwyther S., Mooney M.et al. . New response evaluation criteria in solid tumours: revised RECIST guideline (version 1.1). Eur. J. Cancer. 2009; 45:228–247.
  29. Jubb H.C., Saini H.K., Verdonk M.L., Forbes S.A. COSMIC-3D provides structural perspectives on cancer genetics for drug discovery. Nat. Genet. 2018; 50:1200–1202.
  30. Ju D., Hui D., Hammond D.A., Wonkam A., Tishkoff S.A. Importance of including Non-European populations in large Human genetic studies to enhance precision medicine. Annu. Rev. Biomed. Data Sci. 2022; 5:321–339.
  31. Jia F., Teer J.K., Knepper T.C., Lee J.K., Zhou H.H., He Y.J., McLeod H.L. Discordance of somatic mutations between Asian and Caucasian patient populations with gastric cancer. Mol. Diagn. Ther. 2017; 21:179–185.

Related document on the Qiita

making reference list on biorxiv pdf file
https://qiita.com/kaizen_nagoya/items/75f6f93ce9872a5d622d

Genome modeling and design across all domains of life with evo 2
https://qiita.com/kaizen_nagoya/items/eecda74f758008633ee2

BIOREASON: DNA-LLMモデルによるマルチモーダル生物学的推論の動機付け
https://qiita.com/kaizen_nagoya/items/0718b214043a614deee0

Mckusick’s online mendelian inheritance in man (omim®)
https://qiita.com/kaizen_nagoya/items/c599d867201d1ffb1f4d

Anthropic. Claude 3.7 sonnet
https://qiita.com/kaizen_nagoya/items/4364d9c475114353cf2a

Genomic language models: Opportunities and challenges
https://qiita.com/kaizen_nagoya/items/f797330e64e0c7d05f39

A dna language model based on multispecies alignment predicts the effects of genome-wide variants
https://qiita.com/kaizen_nagoya/items/6e8858c2395dcc98804a

A genomic mutational constraint map using variation in 76,156 human genomes
https://qiita.com/kaizen_nagoya/items/e799ad85ee98bb2a8cf6

Genomic language models: Opportunities and challenges
https://qiita.com/kaizen_nagoya/items/f797330e64e0c7d05f39

Nucleotide transformer: building and evaluating robust foundation models for human genomics
https://qiita.com/kaizen_nagoya/items/1c147c2b095364f04ef7

A genomic mutational constraint map using variation in 76,156 human genomes
https://qiita.com/kaizen_nagoya/items/e799ad85ee98bb2a8cf6

DeepSeek-AI
https://qiita.com/kaizen_nagoya/items/bb5ee9f17c03e07659d8

Codontransformer: A multispecies codon optimizer using context-aware neural networks.
https://qiita.com/kaizen_nagoya/items/d4be1d4dd9eb307f09cc

Medrax: Medical reasoning agent for chest x-ray
https://qiita.com/kaizen_nagoya/items/94c7835b2f461452b2e7

Benchmarking dna foundation models for genomic sequence classification running title: Dna foundation models benchmarking.
https://qiita.com/kaizen_nagoya/items/01e3dde0d8274fee0fd8

Lora: Low-rank adaptation of large language models,
https://qiita.com/kaizen_nagoya/items/877058f681d77808b44c

kegg pull: a software package for the restful access and pulling from the kyoto encyclopedia of gene and genomes.
https://qiita.com/kaizen_nagoya/items/05be40565793f2b4f7f3

Genegpt: augmenting large language models with domain tools for improved access to biomedical information.
https://qiita.com/kaizen_nagoya/items/8897792ff52fb5e68a46

Kegg: biological systems database as a model of the real world.
https://qiita.com/kaizen_nagoya/items/f63573043eaf8f9c6a2c

Entrez direct: E-utilities on the unix command line
https://qiita.com/kaizen_nagoya/items/cc4bbde566e67abc93d9

Clinvar: Public archive of relationships among sequence variation and human phenotype.
https://qiita.com/kaizen_nagoya/items/8149b7a5a4f930490fad

Biobert: a pre-trained biomedical language representation model for biomedical text mining.
https://qiita.com/kaizen_nagoya/items/63781eb6db1fc2ded80a

Progress and opportunities of foundation models in bioinformatics. Briefings in Bioinformatics
https://qiita.com/kaizen_nagoya/items/6ef20eaf796532fed6f8

Bend: Benchmarking dna language models on biologically meaningful tasks.
https://qiita.com/kaizen_nagoya/items/8417e72454d2107a9d06

Hyenadna: Long-range genomic sequence modeling at single nucleotide resolution.
https://qiita.com/kaizen_nagoya/items/07e1ba1138b0825c8a73

Gpt-4o system card.
https://qiita.com/kaizen_nagoya/items/06e4c54af663456b49f9

wen2.5 technical report.
https://qiita.com/kaizen_nagoya/items/f87fac7f9a83f54328fe

Deepseekmath: Pushing the limits of mathematical reasoning in open language models
https://qiita.com/kaizen_nagoya/items/2add7a80056850b9ce87

dbsnp: the ncbi database of genetic variation.
https://qiita.com/kaizen_nagoya/items/756da32e4c0868d84da0

Cosmic: a curated database of somatic variants and clinical data for cancer.
https://qiita.com/kaizen_nagoya/items/2b0960d4e1ff26a9b01f

0
1
0

Register as a new user and use Qiita more conveniently

  1. You get articles that match your needs
  2. You can efficiently read back useful information
  3. You can use dark theme
What you can do with signing up
0
1

Delete article

Deleted articles cannot be recovered.

Draft of this article would be also deleted.

Are you sure you want to delete this article?