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PLoS Genet DOI:10.1371/journal.pgen.1002793

The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits.

Publication TypeJournal Article
Year of Publication2012
AuthorsVoight, 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
JournalPLoS Genet
Volume8
Issue8
Pagese1002793
Date Published2012
ISSN1553-7404
KeywordsAlleles, 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.

URLhttp://dx.plos.org/10.1371/journal.pgen.1002793
DOI10.1371/journal.pgen.1002793
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/22876189?dopt=Abstract

Alternate JournalPLoS Genet.
PubMed ID22876189
PubMed Central IDPMC3410907
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