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Protocols

CCDS specifications

Information


Unique identifier OMICS_01535
Name CCDS
Alternative name Consensus Coding Sequence
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 21.0
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Maintainer


  • person_outline Terence D. Murphy

Publications for Consensus Coding Sequence

CCDS citations

 (62)
call_split

Familial monophasic acute transverse myelitis due to the pathogenic variant in VPS37A

2018
PMCID: 5820602
PMID: 29473047
DOI: 10.1212/NXG.0000000000000213
call_split See protocol

[…] We performed whole-exome sequencing (WES) in 2 affected sisters and their 2 healthy brothers and 1 healthy sister. We captured the consensus coding sequence exonic regions and flanking intronic regions totaling ∼51 Mb using the Agilent SureSelect XT kit and performed paired-end 100 bp reads with the Illumina HiSeq 2500 platform. […]

call_split

Whole genome transcriptomics reveals global effects including up regulation of Francisella pathogenicity island gene expression during active stringent response in the highly virulent Francisella tularensis subsp. tularensis SCHU S4

2017
Microbiology
PMCID: 5845702
PMID: 29034854
DOI: 10.1099/mic.0.000550
call_split See protocol

[…] TopHat in local alignment mode. The short read alignments were used as the input for HTSeq, a python framework for working with high-throughput sequencing data []. Read counts were generated for each consensus coding sequence (CCS) in the reference sequence in HTSeq. Differentially expressed genes were then identified in each condition using the R package DESeq, by comparing the read counts of eac […]

library_books

APPRIS 2017: principal isoforms for multiple gene sets

2017
Nucleic Acids Res
PMCID: 5753224
PMID: 29069475
DOI: 10.1093/nar/gkx997

[…] ence gene set. As a result we have been able to improve the performance of each of the core modules in APPRIS. The gold standard set for principal isoforms are those genes with just one CCDS variant (consensus coding sequence, ). Tests have shown that unique CCDS variants (transcripts annotated consistently by RefSeq and Ensembl/GENCODE manual annotators) and APPRIS principal isoforms are both hig […]

library_books

Liver myofibroblasts of murine origins express mesothelin: Identification of novel rat mesothelin splice variants*

2017
PLoS One
PMCID: 5595315
PMID: 28898276
DOI: 10.1371/journal.pone.0184499

[…] m the DTU-CBS Prediction Servers []. The analysis results are listed in . A multiple alignment of cloned rat Mesothelin splice variant nucleotide sequences was performed with wild-type rat Mesothelin consensus coding sequence (NM_031658.1) as reference, and nucleotide sequence identity (as percentage) determined, using open-access MView tool from the EMBL-EBI bioinformatics web and programmatic to […]

library_books

Annotating pathogenic non coding variants in genic regions

2017
Nat Commun
PMCID: 5550444
PMID: 28794409
DOI: 10.1038/s41467-017-00141-2

[…] genic-assigned training variants (Supplementary Data ).The list of benign variants was obtained from control trios published by Iossifov et al.. All 402 de novo synonymous variants resided within the consensus coding sequence (CCDS) and were identified from individuals not ascertained for any specific disorder. De novo variants were used because they represent novel variants in the gene pool and t […]

library_books

Rare, protein truncating variants in ATM, CHEK2 and PALB2, but not XRCC2, are associated with increased breast cancer risks

2017
J Med Genet
PMCID: 5740532
PMID: 28779002
DOI: 10.1136/jmedgenet-2017-104588

[…] The Fluidigm Access Array 48.48 system was used for library preparation (see online ). We designed 211 amplicons (see online ) to cover 98.1% of the bases within Consensus Coding Sequence (CCDS) exons of the four genes (see online ). Each library of 211 amplicons for 1536 samples was sequenced in 100-base paired-end mode on a single lane of an Illumina Hi-Seq2 […]

Citations

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CCDS institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK; University of California Santa Cruz Genomics Institute, Santa Cruz, CA, USA; Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, USA; HUGO Gene Nomenclature Committee, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
CCDS funding source(s)
Supported by the Intramural Research Program of the National Institutes of Health, National Library of Medicine, the Wellcome Trust [WT098051, WT108749/Z/15/Z], the National Human Genome Research Institute (NHGRI) [U41HG007234, 2U41HG007234], the European Molecular Biology Laboratory, an NHGRI grant [U41HG003345], a Wellcome Trust grant [099129/Z/12/Z], an NHGRI grant [U41HG000330] and the NHGRI grant for the GENCODE project [U41HG007234].

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