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Cited by 147Genomics and Phylogenetic StudiesBiomedical Text Mining and OntologiesGenomics and Rare Diseases

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation

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Pujar, Shashikant, O’Leary, Nuala A, Farrell, Catherine M, Loveland, Jane E, Mudge, Jonathan M, Wallin, Craig, Girón, Carlos G, Diekhans, Mark +29 more·2018·Nucleic Acids Research
DOI 10.1093/nar/gkx1031PMC PMC5753299
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Abstract

The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community.

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  • They excluded 118 sequences with VerifyBAMID freemix ≥4% and 5 sequences with less than 94.5% of CCDS achieving tenfold read depth.

    “We excluded from analyses 118 (0.025%) sequences that achieved a VerifyBAMID freemix (contamination) level of 4% or higher68, and an additional five sequences (0.001%) where less than 94.5% of the CCDS (release 22) achieved a minimum of tenfold read depth69.”

    From Rare variant associations with plasma protein levels in the UK Biobank (2023) · cites this paper as [69]

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Authors
Pujar, S., O’Leary, N. A., Farrell, C. M., Loveland, J. E., Mudge, J. M., Wallin, C., Girón, C. G., Diekhans, M., Barnes, I., Bennett, R., Berry, A. E., Cox, E., Davidson, C., Goldfarb, T., Gonzalez, J. M., Hunt, T., Jackson, J., Joardar, V., Kay, M. P., Kodali, V. K., Martin, F. J., McAndrews, M., McGarvey, K. M., Murphy, M., Rajput, B., Rangwala, S. H., Riddick, L. D., Seal, R. L., Suner, M.-M., Webb, D., Zhu, S., Aken, B. L., Bruford, E. A., Bult, C. J., Frankish, A., Murphy, T., & Pruitt, K. D.
Affiliations
  • National Institutes of Health (US)
  • European Bioinformatics Institute (GB)
  • University of California, Santa Cruz (US)
  • Jackson Laboratory (US)
Corresponding author
Murphy, Terence
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2017-11-06
Volume
46
Issue
D1
Pages
D221-D228
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkx1031
PMC
PMC5753299
OpenAlex
W2767232866
Cited by
147
References
2
Citations by year
2026: 15 · 2025: 24 · 2024: 15 · 2023: 25 · 2022: 24 · 2021: 20 · 2020: 14 · 2019: 6 · 2018: 4
FWCI
2.68
Type
journal article
Language
en
Open access
Licence
public-domain
Locations
  • Nucleic Acids Research (publishedVersion, public-domain)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion, cc-by-nc)
Funders
  • Wellcome Trust (WT 098051, WT108749/Z/15/Z, 099129/Z/12/Z)
  • European Bioinformatics Institute
  • National Human Genome Research Institute (U41HG007234, U41HG003345)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
Keywords
protein-coding regions, human genome annotation, expert curation, reference genome, Mouse Genome Informatics, Ensembl, NCBI
MeSH terms
Animals, Humans, National Library of Medicine (U.S.), United States, User-Computer Interface, Open Reading Frames, Consensus Sequence, Guidelines as Topic, Databases, Genetic, Mice, Molecular Sequence Annotation, Data Curation

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