The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits
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The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits. / Voight, Benjamin F; Kang, Hyun Min; Ding, Jun; Palmer, Cameron D; Sidore, Carlo; Chines, Peter S; Burtt, Noël P; Fuchsberger, Christian; Li, Yanming; Erdmann, Jeanette; Frayling, Timothy M; Heid, Iris M; Jackson, Anne U; Johnson, Toby; Oskari Kilpeläinen, Tuomas; Lindgren, Cecilia M; Morris, Andrew P; Prokopenko, Inga; Randall, Joshua C; Saxena, Richa; Soranzo, Nicole; Speliotes, Elizabeth K; Teslovich, Tanya M; Wheeler, Eleanor; Maguire, Jared; Parkin, Melissa; Potter, Simon; Rayner, N William; Robertson, Neil; Stirrups, Kathleen; Winckler, Wendy; Sanna, Serena; Mulas, Antonella; Nagaraja, Ramaiah; Cucca, Francesco; Barroso, Inês; Deloukas, Panos; Loos, Ruth J F; Kathiresan, Sekar; Munroe, Patricia B; Newton-Cheh, Christopher; Pfeufer, Arne; Samani, Nilesh J; Schunkert, Heribert; Hirschhorn, Joel N; Altshuler, David; McCarthy, Mark I; Abecasis, Gonçalo R; Boehnke, Michael.
In: P L o S Genetics (Online), Vol. 8, No. 8, 2012, p. e1002793.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits
AU - Voight, Benjamin F
AU - Kang, Hyun Min
AU - Ding, Jun
AU - Palmer, Cameron D
AU - Sidore, Carlo
AU - Chines, Peter S
AU - Burtt, Noël P
AU - Fuchsberger, Christian
AU - Li, Yanming
AU - Erdmann, Jeanette
AU - Frayling, Timothy M
AU - Heid, Iris M
AU - Jackson, Anne U
AU - Johnson, Toby
AU - Oskari Kilpeläinen, Tuomas
AU - Lindgren, Cecilia M
AU - Morris, Andrew P
AU - Prokopenko, Inga
AU - Randall, Joshua C
AU - Saxena, Richa
AU - Soranzo, Nicole
AU - Speliotes, Elizabeth K
AU - Teslovich, Tanya M
AU - Wheeler, Eleanor
AU - Maguire, Jared
AU - Parkin, Melissa
AU - Potter, Simon
AU - Rayner, N William
AU - Robertson, Neil
AU - Stirrups, Kathleen
AU - Winckler, Wendy
AU - Sanna, Serena
AU - Mulas, Antonella
AU - Nagaraja, Ramaiah
AU - Cucca, Francesco
AU - Barroso, Inês
AU - Deloukas, Panos
AU - Loos, Ruth J F
AU - Kathiresan, Sekar
AU - Munroe, Patricia B
AU - Newton-Cheh, Christopher
AU - Pfeufer, Arne
AU - Samani, Nilesh J
AU - Schunkert, Heribert
AU - Hirschhorn, Joel N
AU - Altshuler, David
AU - McCarthy, Mark I
AU - Abecasis, Gonçalo R
AU - Boehnke, Michael
PY - 2012
Y1 - 2012
N2 - 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.
AB - 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.
KW - Alleles
KW - Anthropometry
KW - Cardiovascular Diseases
KW - Diabetes Mellitus, Type 2
KW - Gene Frequency
KW - Genome, Human
KW - Genome-Wide Association Study
KW - Genotype
KW - Genotyping Techniques
KW - Humans
KW - Metabolomics
KW - Oligonucleotide Array Sequence Analysis
KW - Phenotype
KW - Polymorphism, Single Nucleotide
KW - Quantitative Trait Loci
U2 - 10.1371/journal.pgen.1002793
DO - 10.1371/journal.pgen.1002793
M3 - Journal article
C2 - 22876189
VL - 8
SP - e1002793
JO - P L o S Genetics
JF - P L o S Genetics
SN - 1553-7390
IS - 8
ER -
ID: 46278632