title: The GENCODE exome: sequencing the complete human exome.
abstract: 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.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
authors.forename: Alison J
authors.initials: AJ
authors.lastname: Coffey
authors.forename: Felix
authors.initials: F
authors.lastname: Kokocinski
authors.forename: Maria S
authors.initials: MS
authors.lastname: Calafato
authors.forename: Carol E
authors.initials: CE
authors.lastname: Scott
authors.forename: Priit
authors.initials: P
authors.lastname: Palta
authors.forename: Eleanor
authors.initials: E
authors.lastname: Drury
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Joyce
authors.forename: Emily M
authors.initials: EM
authors.lastname: Leproust
authors.forename: Jen
authors.initials: J
authors.lastname: Harrow
authors.forename: Sarah
authors.initials: S
authors.lastname: Hunt
authors.forename: Anna-Elina
authors.initials: AE
authors.lastname: Lehesjoki
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Turner
authors.forename: Tim J
authors.initials: TJ
authors.lastname: Hubbard
authors.forename: Aarno
authors.initials: A
authors.lastname: Palotie
mesh_terms: D019295:Computational Biology; D016384:Consensus Sequence / Q000235:genetics; D030541:Databases, Genetic; D005091:Exons / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics*; D023281:Genomics; D006801:Humans; D016366:Open Reading Frames / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA