The GENCODE exome: sequencing the complete human exome

Sequencing the coding regions, the exome, of the human genome is one of the major current strategies to identify low frequency and rare variants associated with human disease traits. So far, the most widely used commercial exome capture reagents have mainly targeted the consensus coding sequence (CC...

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Bibliographic Details
Published in:European journal of human genetics : EJHG 2011-07, Vol.19 (7), p.827-831
Main Authors: COFFEY, Alison J, KOKOCINSKI, Felix, LEHESJOKI, Anna-Elina, TURNER, Daniel J, HUBBARD, Tim J, PALOTIE, Aarno, CALAFATO, Maria S, SCOTT, Carol E, PALTA, Priit, DRURY, Eleanor, JOYCE, Christopher J, LEPROUST, Emily M, HARROW, Jen, HUNT, Sarah
Format: Article
Language:English
Subjects:
Annotations
Bioinformatics
Biological and medical sciences
Channel gating
Collaboration
Computational Biology
Consensus Sequence - genetics
Conserved sequence
Consortia
Databases, Genetic
Deoxyribonucleic acid
Design
Disease
DNA
Exons - genetics
Fundamental and applied biological sciences. Psychology
General aspects. Genetic counseling
Genes
Genetics
Genetics of eukaryotes. Biological and molecular evolution
Genome, Human - genetics
Genomes
Genomics
Humans
Kinases
Medical genetics
Medical sciences
Molecular and cellular biology
Open Reading Frames - genetics
Polymorphism, Single Nucleotide - genetics
Protein kinase
Proteins
Sequence Analysis, DNA
Short Report
Single-nucleotide polymorphism
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Summary:Sequencing the coding regions, the exome, of the human genome is one of the major current strategies to identify low frequency and rare variants associated with human disease traits. So far, the most widely used commercial exome capture reagents have mainly targeted the consensus coding sequence (CCDS) database. We report the design of an extended set of targets for capturing the complete human exome, based on annotation from the GENCODE consortium. The extended set covers an additional 5594 genes and 10.3 Mb compared with the current CCDS-based sets. The additional regions include potential disease genes previously inaccessible to exome resequencing studies, such as 43 genes linked to ion channel activity and 70 genes linked to protein kinase activity. In total, the new GENCODE exome set developed here covers 47.9 Mb and performed well in sequence capture experiments. In the sample set used in this study, we identified over 5000 SNP variants more in the GENCODE exome target (24%) than in the CCDS-based exome sequencing.
ISSN:1018-4813
1476-5438
1476-5438
DOI:10.1038/ejhg.2011.28