Publication Type | Journal Article |
Year of Publication | 2012 |
Authors | Voight, BF, Kang, HMin, Ding, J, Palmer, CD, Sidore, C, Chines, PS, Burtt, NP, Fuchsberger, C, Li, Y, Erdmann, J, Frayling, TM, Heid, IM, Jackson, AU, Johnson, T, Kilpeläinen, TO, Lindgren, CM, Morris, AP, Prokopenko, I, Randall, JC, Saxena, R, Soranzo, N, Speliotes, EK, Teslovich, TM, Wheeler, E, Maguire, J, Parkin, M, Potter, S, N Rayner, W, Robertson, N, Stirrups, K, Winckler, W, Sanna, S, Mulas, A, Nagaraja, R, Cucca, F, Barroso, I, Deloukas, P, Loos, RJF, Kathiresan, S, Munroe, PB, Newton-Cheh, C, Pfeufer, A, Samani, NJ, Schunkert, H, Hirschhorn, JN, Altshuler, D, McCarthy, MI, Abecasis, GR, Boehnke, M |
Journal | PLoS Genet |
Volume | 8 |
Issue | 8 |
Pages | e1002793 |
Date Published | 2012 |
ISSN | 1553-7404 |
Keywords | Alleles, Anthropometry, Cardiovascular Diseases, Diabetes Mellitus, Type 2, Gene Frequency, Genome, Human, Genome-Wide Association Study, Genotype, Genotyping Techniques, Humans, Metabolomics, Oligonucleotide Array Sequence Analysis, Phenotype, Polymorphism, Single Nucleotide, Quantitative Trait Loci |
Abstract | Genome-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. |
URL | http://dx.plos.org/10.1371/journal.pgen.1002793 |
DOI | 10.1371/journal.pgen.1002793 |
Pubmed | |
Alternate Journal | PLoS Genet. |
PubMed ID | 22876189 |
PubMed Central ID | PMC3410907 |
Grant List | / / British Heart Foundation / United Kingdom N01-AG-1-2109 / AG / NIA NIH HHS / United States R01 HG000376 / HG / NHGRI NIH HHS / United States 090532 / / Wellcome Trust / United Kingdom 098051 / / Wellcome Trust / United Kingdom 064890 / / Wellcome Trust / United Kingdom DK062370 / DK / NIDDK NIH HHS / United States HG005214 / HG / NHGRI NIH HHS / United States P30 DK020572 / DK / NIDDK NIH HHS / United States HG005581 / HG / NHGRI NIH HHS / United States MC_U106188470 / / Medical Research Council / United Kingdom 081682 / / Wellcome Trust / United Kingdom HG000376 / HG / NHGRI NIH HHS / United States |
PLoS Genet DOI:10.1371/journal.pgen.1002793
The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits.
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