The GENCODE exome - sequencing the complete human exome

Aarno Palotie (1) , Alison J Coffey (1) , Felix Kokocinski (1) , Maria S Calafato (1) , Carol E Scott (1) , Priit Palta (1) , Eleanor Drury (1) , Christopher J Joyce (1) , Emily M Leproust (1) , Jen Harrow (1) , Sarah Hunt (1) , Anna-Elina Lehesjoki (1) , Daniel J Turner (1) , Tim Hubbard (1)

1 Head of Medical Sequencing

Sequencing the coding regions, the exome, of the human genome is a 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 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 5,594 genes and 10.3 Mb compared to 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 5,000 SNP variants more in the GENCODE exome target (24%) than in the CCDS-based exome sequencing.

Mots clés: human exome; resequencing; GENCODE

Aarno Palotie, Alison J Coffey, Felix Kokocinski, Maria S Calafato, Carol E Scott, et al.. The GENCODE exome - sequencing the complete human exome. European Journal of Human Genetics, 2011, ⟨10.1038/ejhg.2011.28⟩. ⟨hal-00618485⟩