Dataset Information

GENCODE: the reference human genome annotation for The ENCODE Project.

ABSTRACT: The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.

SUBMITTER: Harrow J

PROVIDER: S-EPMC3431492 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature

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GENCODE: the reference human genome annotation for The ENCODE Project.

Harrow Jennifer J Frankish Adam A Gonzalez Jose M JM Tapanari Electra E Diekhans Mark M Kokocinski Felix F Aken Bronwen L BL Barrell Daniel D Zadissa Amonida A Searle Stephen S Barnes If I Bignell Alexandra A Boychenko Veronika V Hunt Toby T Kay Mike M Mukherjee Gaurab G Rajan Jeena J Despacio-Reyes Gloria G Saunders Gary G Steward Charles C Harte Rachel R Lin Michael M Howald Cédric C Tanzer Andrea A Derrien Thomas T Chrast Jacqueline J Walters Nathalie N Balasubramanian Suganthi S Pei Baikang B Tress Michael M Rodriguez Jose Manuel JM Ezkurdia Iakes I van Baren Jeltje J Brent Michael M Haussler David D Kellis Manolis M Valencia Alfonso A Reymond Alexandre A Gerstein Mark M Guigó Roderic R Hubbard Tim J TJ

Genome research 20120901 9

The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented i ...[more]

PMID: 22955987

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Project description:BackgroundA vast amount of DNA variation is being identified by increasingly large-scale exome and genome sequencing projects. To be useful, variants require accurate functional annotation and a wide range of tools are available to this end. McCarthy et al recently demonstrated the large differences in prediction of loss-of-function (LoF) variation when RefSeq and Ensembl transcripts are used for annotation, highlighting the importance of the reference transcripts on which variant functional annotation is based.ResultsWe describe a detailed analysis of the similarities and differences between the gene and transcript annotation in the GENCODE and RefSeq genesets. We demonstrate that the GENCODE Comprehensive set is richer in alternative splicing, novel CDSs, novel exons and has higher genomic coverage than RefSeq, while the GENCODE Basic set is very similar to RefSeq. Using RNAseq data we show that exons and introns unique to one geneset are expressed at a similar level to those common to both. We present evidence that the differences in gene annotation lead to large differences in variant annotation where GENCODE and RefSeq are used as reference transcripts, although this is predominantly confined to non-coding transcripts and UTR sequence, with at most ~30% of LoF variants annotated discordantly. We also describe an investigation of dominant transcript expression, showing that it both supports the utility of the GENCODE Basic set in providing a smaller set of more highly expressed transcripts and provides a useful, biologically-relevant filter for further reducing the complexity of the transcriptome.ConclusionsThe reference transcripts selected for variant functional annotation do have a large effect on the outcome. The GENCODE Comprehensive transcripts contain more exons, have greater genomic coverage and capture many more variants than RefSeq in both genome and exome datasets, while the GENCODE Basic set shows a higher degree of concordance with RefSeq and has fewer unique features. We propose that the GENCODE Comprehensive set has great utility for the discovery of new variants with functional potential, while the GENCODE Basic set is more suitable for applications demanding less complex interpretation of functional variants.

Dataset Information

GENCODE: the reference human genome annotation for The ENCODE Project.

Publications

GENCODE: the reference human genome annotation for The ENCODE Project.

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