The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits.
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 o...
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2012
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oai:doaj.org-article:21b726bfdf0a4eefa0620b05e0aec27d2021-11-18T06:18:18ZThe metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits.1553-73901553-740410.1371/journal.pgen.1002793https://doaj.org/article/21b726bfdf0a4eefa0620b05e0aec27d2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22876189/pdf/?tool=EBIhttps://doaj.org/toc/1553-7390https://doaj.org/toc/1553-7404Genome-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.Benjamin F VoightHyun Min KangJun DingCameron D PalmerCarlo SidorePeter S ChinesNoël P BurttChristian FuchsbergerYanming LiJeanette ErdmannTimothy M FraylingIris M HeidAnne U JacksonToby JohnsonTuomas O KilpeläinenCecilia M LindgrenAndrew P MorrisInga ProkopenkoJoshua C RandallRicha SaxenaNicole SoranzoElizabeth K SpeliotesTanya M TeslovichEleanor WheelerJared MaguireMelissa ParkinSimon PotterN William RaynerNeil RobertsonKathleen StirrupsWendy WincklerSerena SannaAntonella MulasRamaiah NagarajaFrancesco CuccaInês BarrosoPanos DeloukasRuth J F LoosSekar KathiresanPatricia B MunroeChristopher Newton-ChehArne PfeuferNilesh J SamaniHeribert SchunkertJoel N HirschhornDavid AltshulerMark I McCarthyGonçalo R AbecasisMichael BoehnkePublic Library of Science (PLoS)articleGeneticsQH426-470ENPLoS Genetics, Vol 8, Iss 8, p e1002793 (2012) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Genetics QH426-470 |
| spellingShingle |
Genetics QH426-470 Benjamin F Voight Hyun Min Kang Jun Ding Cameron D Palmer Carlo Sidore Peter S Chines Noël P Burtt Christian Fuchsberger Yanming Li Jeanette Erdmann Timothy M Frayling Iris M Heid Anne U Jackson Toby Johnson Tuomas O Kilpeläinen Cecilia M Lindgren Andrew P Morris Inga Prokopenko Joshua C Randall Richa Saxena Nicole Soranzo Elizabeth K Speliotes Tanya M Teslovich Eleanor Wheeler Jared Maguire Melissa Parkin Simon Potter N William Rayner Neil Robertson Kathleen Stirrups Wendy Winckler Serena Sanna Antonella Mulas Ramaiah Nagaraja Francesco Cucca Inês Barroso Panos Deloukas Ruth J F Loos Sekar Kathiresan Patricia B Munroe Christopher Newton-Cheh Arne Pfeufer Nilesh J Samani Heribert Schunkert Joel N Hirschhorn David Altshuler Mark I McCarthy Gonçalo R Abecasis Michael Boehnke The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits. |
| description |
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. |
| format |
article |
| author |
Benjamin F Voight Hyun Min Kang Jun Ding Cameron D Palmer Carlo Sidore Peter S Chines Noël P Burtt Christian Fuchsberger Yanming Li Jeanette Erdmann Timothy M Frayling Iris M Heid Anne U Jackson Toby Johnson Tuomas O Kilpeläinen Cecilia M Lindgren Andrew P Morris Inga Prokopenko Joshua C Randall Richa Saxena Nicole Soranzo Elizabeth K Speliotes Tanya M Teslovich Eleanor Wheeler Jared Maguire Melissa Parkin Simon Potter N William Rayner Neil Robertson Kathleen Stirrups Wendy Winckler Serena Sanna Antonella Mulas Ramaiah Nagaraja Francesco Cucca Inês Barroso Panos Deloukas Ruth J F Loos Sekar Kathiresan Patricia B Munroe Christopher Newton-Cheh Arne Pfeufer Nilesh J Samani Heribert Schunkert Joel N Hirschhorn David Altshuler Mark I McCarthy Gonçalo R Abecasis Michael Boehnke |
| author_facet |
Benjamin F Voight Hyun Min Kang Jun Ding Cameron D Palmer Carlo Sidore Peter S Chines Noël P Burtt Christian Fuchsberger Yanming Li Jeanette Erdmann Timothy M Frayling Iris M Heid Anne U Jackson Toby Johnson Tuomas O Kilpeläinen Cecilia M Lindgren Andrew P Morris Inga Prokopenko Joshua C Randall Richa Saxena Nicole Soranzo Elizabeth K Speliotes Tanya M Teslovich Eleanor Wheeler Jared Maguire Melissa Parkin Simon Potter N William Rayner Neil Robertson Kathleen Stirrups Wendy Winckler Serena Sanna Antonella Mulas Ramaiah Nagaraja Francesco Cucca Inês Barroso Panos Deloukas Ruth J F Loos Sekar Kathiresan Patricia B Munroe Christopher Newton-Cheh Arne Pfeufer Nilesh J Samani Heribert Schunkert Joel N Hirschhorn David Altshuler Mark I McCarthy Gonçalo R Abecasis Michael Boehnke |
| author_sort |
Benjamin F Voight |
| title |
The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits. |
| title_short |
The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits. |
| title_full |
The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits. |
| title_fullStr |
The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits. |
| title_full_unstemmed |
The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits. |
| title_sort |
metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2012 |
| url |
https://doaj.org/article/21b726bfdf0a4eefa0620b05e0aec27d |
| work_keys_str_mv |
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