The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.

By Kim D. Pruitt, J. Harrow, Rachel A. Harte, Craig Wallin, Mark Diekhans, Donna R. Maglott, S. Searle, C. Farrell, J. Loveland, B. Ruef and 39 more. Genome Research, 2009

586 citations recorded by the source corpus.

Effective use of the human and mouse genomes requires reliable identification of genes and their products. Although multiple public resources provide annotation, different methods are used that can result in similar but not identical representation of genes, transcripts, and proteins. The collaborative consensus coding sequence (CCDS) project tracks identical protein annotations on the reference mouse and human genomes with a stable identifier (CCDS ID), and ensures that they are consistently represented on the NCBI, Ensembl, and UCSC Genome Browsers. Importantly, the project coordinates on manually reviewing inconsistent protein annotations between sites, as well as annotations for which new evidence suggests a revision is needed, to progressively converge on a complete protein-coding set for the human and mouse reference genomes, while maintaining a high standard of reliability and biological accuracy. To date, the project has identified 20,159 human and 17,707 mouse consensus coding regions from 17,052 human and 16,893 mouse genes. Three evaluation methods indicate that the entries in the CCDS set are highly likely to represent real proteins, more so than annotations from contributing groups not included in CCDS. The CCDS database thus centralizes the function of identifying well-supported, identically-annotated, protein-coding regions.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/fd9e26e26588f060b270e9b5856f050be540bc03

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Citations in the corpus

Ensembl 2011 (2010, methodology): “We continue to work with the CCDS project for both human and mouse gene sets (26) using the gene models described here as our input to the project and identifying those genes in our databases that are part of the CCDS sets.”
Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes (2013, unknown): “Only mutations reported in CCDS transcripts [17] were considered.”
The Ensembl gene annotation system (2016, unknown): “Ensembl collaborates in the Consensus Coding Sequence (CCDS) project (90, 91).”
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy (2011, background): “cgi (9)] is a central hub for curation of protein-coding loci and all”
Exome sequencing identifies the cause of a Mendelian disorder (2009, unknown): “The exome was conservatively defined using the NCBI Consensus Coding Sequence (CCDS) database 9 (version 20080902), which covers approximately 164,000 noncontiguous regions over 27.9 Mb, of which 26.6 Mb were ‘mappable’ using 76-bp single-end reads.”
The Universal Protein Resource (UniProt) in 2010 (2009, background): “UniProt recently joined the Consensus CDS (CCDS) project (13), a collaborative effort to identify a core set of consistently annotated and high quality human and mouse protein-coding regions.”
The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity (2015, methodology): “We used Consensus Coding Sequence (CCDS) release 14 as the set of protein-coding genes of interest for scoring noncoding intolerance [44].”
Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues (2013, background): “Almost all of these events (25,920) were found in comparisons between different tissues, although a significant fraction (16,382) were also found when comparing isoforms within the same tissue.”
The UCSC Genome Browser database: extensions and updates 2013 (2012, background): “Additionally, for most organisms we show alignments from RefSeq genes (3), mRNAs and ESTs from GenBank (4), and other gene or gene prediction tracks such as Ensembl Genes (5).”
GENCODE: The reference human genome annotation for The ENCODE Project (2012, methodology): “We compared the composition of annotation across the five major gene sets publicly available in UCSC, GENCODE, CCDS, RefSeq, and AceView.”
Database resources of the National Center for Biotechnology Information (2006, methodology): “The conserved CDS database (CCDS) project is a collaborative effort among NCBI, the European Bioinformatics Institute, the Wellcome Trust Sanger Institute and University of California, Santa Cruz (UCSC) to identify a set of human and mouse protein coding regions that are consistently annotated and o”
The UCSC Genome Browser database: 2014 update (2013, background): “The UCSC Genes track, which includes protein-coding genes and non-coding RNA genes from RefSeq, GenBank, CCDS (12), Rfam (13) and the tRNA Genes track (14), was updated on both the GRCh37/hg19 human and GRCm38/mm10 mouse assemblies.”
The UCSC Genome Browser database: update 2010 (2009, background): “Other tracks that are updated each night include the Mammalian Gene Collection (MGC) tracks (18) on the human, mouse, rat, cow and frog browsers, the Consensus Coding Sequence (CCDS) tracks (19) on the human and mouse, and the ORFeome Clones tracks (which show alignments of clones from the ORFeome C”
dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Non-synonymous and Splice Site SNVs (2016, methodology): “0 [Liu et al., 2011] was based on the human reference sequence version hg18 and the gene model of Consensus Coding Sequence (CCDS) version 20090327 [Pruitt et al., 2009].”