EGAGenomicsIllumina HumanExome-12v1_A-GenCall, zCall, GenoSNP, - IlluminusGenotypehttps://ega-archive.org/studies/EGAS00000000115EGAEGA study EGAS00000000115Title not providedrestrictedEGAGenome-wide association studies have identified hundreds of loci for type 2 diabetes, coronary artery disease and myocardial infarction, as well as for related traits such as body mass index, glucose and insulin levels, lipid levels, and blood pressure. These studies also have pointed to thousands of loci with promising but not yet compelling association evidence. To establish association at additional loci and to characterize the genome-wide significant loci by fine-mapping, we designed the "Metabochip," a custom genotyping array that assays nearly 200,000 SNP markers. Here, we describe the Metabochip and its component SNP sets, evaluate its performance in capturing variation across the allele-frequency spectrum, describe solutions to methodological challenges commonly encountered in its analysis, and evaluate its performance as a platform for genotype imputation. The metabochip achieves dramatic cost efficiencies compared to designing single-trait follow-up reagents, and provides the opportunity to compare results across a range of related traits. The metabochip and similar custom genotyping arrays offer a powerful and cost-effective approach to follow-up large-scale genotyping and sequencing studies and advance our understanding of the genetic basis of complex human diseases and traits.The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits.Voight Benjamin F BF, Kang Hyun Min HM, Ding Jun J, Palmer Cameron D CD, Sidore Carlo C, Chines Peter S PS, Burtt Noël P NP, Fuchsberger Christian C, Li Yanming Y, Erdmann Jeanette J, Frayling Timothy M TM, Heid Iris M IM, Jackson Anne U AU, Johnson Toby T, Kilpeläinen Tuomas O TO, Lindgren Cecilia M CM, Morris Andrew P AP, Prokopenko Inga I, Randall Joshua C JC, Saxena Richa R, Soranzo Nicole N, Speliotes Elizabeth K EK, Teslovich Tanya M TM, Wheeler Eleanor E, Maguire Jared J, Parkin Melissa M, Potter Simon S, Rayner N William NW, Robertson Neil N, Stirrups Kathleen K, Winckler Wendy W, Sanna Serena S, Mulas Antonella A, Nagaraja Ramaiah R, Cucca Francesco F, Barroso Inês I, Deloukas Panos P, Loos Ruth J F RJ, Kathiresan Sekar S, Munroe Patricia B PB, Newton-Cheh Christopher C, Pfeufer Arne A, Samani Nilesh J NJ, Schunkert Heribert H, Hirschhorn Joel N JN, Altshuler David D, McCarthy Mark I MI, Abecasis Gonçalo R GR, Boehnke Michael MfalseAssociation studies using the Metabochip array - Samples analysed by the WTCCC (1958 British Birth Cohort (58BC), Hypertension cohort (HT), Type 2 Diabetes Cohort (T2D) and Coronary Artery Disease (CAD) cohort)Genomewide association studies (GWAS) have proven a powerful hypothesis-free method to identify common disease-associated variants. Even quite large GWAS, however, have only at best identified moderate proportions of the genetic variants contributing to disease heritability. To provide cost-effective genotyping of common and rare variants to map the remaining heritability and to fine-map established loci, the Metabochip Consortium has developed a 200,000 SNP chip that has been produced in very large numbers for a fraction of the cost of GWAS chips. This chip provides a powerful tool for genetic studies of metabolic, cardiovascular and anthropometric traits (Voight et al., in press PLoS Genetics).2019-10-31 12:52:09EGAS00000000115960622876189EGAD00010000232EGAD00010000234EGAD00010000230EGAD00010000236EGAC00001000205