{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"technology_type":["Illumina HumanExome-12v1_A-GenCall, zCall, GenoSNP, - Illuminus"],"study_type":["Genotype"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00000000115"],"host":["EGA"],"description":["EGA study EGAS00000000115"],"dataset_title":["Title not provided"],"category":["restricted"],"repository":["EGA"],"pubmed_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."],"pubmed_title":["The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits."],"pubmed_authors":["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 M"],"name_synonyms":["Adult-Onset Diabetes Mellitus, Diabetes Type 2, type 2, DmelCG9414, Type 2 Diabetes Mellitus, fs(1)M34, E-Cadherin, Coronary, diabetes mellitus type 2, csp2, Associations, drep4, Non-Insulin Dependent Diabetes Mellitus, Maturity Onset Diabetes, cold antibody disease, CG4601, Caspase-activated nuclease, Slow Onset, Left Main Coronary Artery Disease, 5730477D02Rik, Coronary Arteriosclerosis, 4.1.1.6, DHO, DCAD2, DCad2, CG18572, cold antibody, S67, Immune-responsive gene 1 protein, DECad, CG3722, Ketosis-Resistant Diabetes Mellitus, NIDDM, DFF40, cd, DE Cad, Noninsulin-Dependent, Diabetes mellitus, DE-CAD2, dEcad, 38E.19, MODY (Maturity-onset diabetes of the young), ACT, DECadh, Childbirths, Non Insulin Dependent, DEcad, DE, Left Main Coronary Disease, anon-WO2004063362.83, Drep4, Adult-onset diabetes mellitus, High Blood Pressures, Shg, Caspase-activated DNase, DE-Cad2, High blood pressure, collisionally activated dissociation, Noninsulin-dependent diabetes mellitus, CID, DE-cadh, Adult-Onset, Adult-Onset Diabetes, Su(b), ECadh, DE-Cadherin, anemia, Didff, DE-cadherin, DFF2, Coronary Arterioscleroses, Ketosis Resistant, CG9414, 40kDa, GAT, Maturity-Onset Diabetes Mellitus, HTN, shg/DE-Cad, D E-cad, cold antibody hemolytic anaemia, E-cadherin, Caspase-activated deoxyribonuclease, Type II Diabetes, Atherosclerosis, Type 2, AI323667, gp150, hemolytic, Hypertension, DFF-40, Noninsulin-Dependent Diabetes Mellitus, type II, non-insulin-dependent, Non-Insulin Dependent Diabetes, Artery Disease, DmelCG3722, Cis-aconitic acid decarboxylase, dCAD, microarray, CT12481, Slow-Onset, com5, hypertension, DCad, ECad2, Childbirth, l(1)Ab, T2DM - Type 2 Diabetes mellitus, DE Cadh, AU018859, Noninsulin Dependent, Parturitions, DIABETES MELLITUS TYPE 02, 3.-.-.-, Maturity-onset diabetes, l(2)10469, l(2)k03401, Births, Blood Pressures, Non-Insulin-Dependent, Arterioscleroses, non-insulin-dependent diabetes mellitus, Maturity-Onset Diabetes, Blood Pressure, CadE, T2DM, Ecad, CPAN, Birth, cadh, Coronary Atheroscleroses, Non-Insulin-Dependent Diabetes Mellitus, DmelCG1759, Cpad, Atheroscleroses, Coronary Artery Diseases, Maturity Onset Diabetes Mellitus, adult-onset, fs(1)829, ECAD, ECad, 2410008J01Rik, Maturity-onset diabetes mellitus, Noninsulin Dependent Diabetes Mellitus, Stable, D-cad, Diabetes Mellitus, DmelCG18572, Rep4, Ketosis-Resistant, Diabetes, High Blood Pressure, CADH, Adult Onset, Type 2 diabetes, DE[cyto], coronary arteriosclerosis, CPS, Adult-onset diabetes, Type 2 diabetes mellitus, Left Main Disease, cold antibody hemolytic anemia, DREP-4, DE-cad, MODY, Cadh, N-cad, T2D, CAD, Cad, Slow-Onset Diabetes Mellitus, Maturity-Onset, DE-CAD, DE-Cad, Type 2 Diabetes Mellitus Non-Insulin Dependent, Arteriosclerosis, Left Main Diseases, Aconitate decarboxylase, l(2)k10220., Type 2 Diabetes, DNA fragmentation factor 40 kDa subunit, cad, Artery Diseases, PYR1, Coronary Atherosclerosis, E-cad, High, DEC, Coronary Artery Disease, DRORUD, Type II, CG1759, Stable Diabetes Mellitus, e-cad, Maturity Onset, E-CAD, E-Cad"],"description_synonyms":["HSPABP2, other disease, dmBest1, Procedures, methionine aminopeptidase activity, acetylglucosaminyltransferase-like protein, BEST1, 2210017D18Rik, dCHIP, Mbp1, Cost Comparisons, SCAR16, Measure, CG30327, anon-WO0118547.380, LARGE1, DmelCG6264, Cost-Minimization, froggy, Gyltl1a, CG11478, method, Techniques, DmelCG5203, diseases, Cost Minimization Analysis, Method, Associations, method used in an experiment, Studies, disease or disorder, ARB, 2, diseases and disorders, Analysis, myd, Cost Comparison, Technique, BEST1_HUMAN, 2310040B03Rik, familial adenomatous polyposis, MAP, peptidase M activity, adenomas, rabGAPLP, DmelCG42257, human disease, L-methionine aminopeptidase activity, NY-CO-7, like-acetylglucosaminyltransferase, Analyses, Cost Measures, Chip, ChIP, MDDGB6, VMD2, Cost-Minimization Analyses, Affordability, familial adenomatous polyposis 2, CHIP, Mbp-1, Measures, RabGAP-5, Comparison, anthropometric traits, LARGE, BMD, financing, free, non-neoplastic, genetic, autosomal recessive multiple colorectal adenomas, Study, BPFD#36, Cost Analysis, funding, chip, Methodological Studies, RUSC3, 65K, DmelCG3924, CG42257, Dmel_CG30327, AW046544, disorder, Homo sapiens disease, snp, Comparisons, UBOX1, associated, Affordabilities, 0610033N24Rik, constitutitional genetic, PP1131, RP50, vitelliform macular dystrophy 2 (Best disease, fees, heredity., cg11478, anthropometry, l(2)k04405, CG6264, MUTYH-Associated Polyposis, gyltl1b-b, disorders, familial, MYH-associated polyposis, autosomal recessive familial adenomatous polyposis, CG5203, Maps, medical condition, Procedure, l(2)04405, MDDGA6, mKIAA0609, CG6393, Diseases, condition, rare (European definition), KIAA0609, TU15B, acetylglucosaminyltransferase-like 1A, bestrophin), finances, autosomal recessive, SDCCAG7, dBest1, Costs and Cost Analyses, fg, Costs, RUTBC3, Dmel_CG6393, Dbest, gyltl1b, dLdb, best, Ldb, LDB, Cost, dbest1, mdc1d, Cost-Minimization Analysis, salaries, common, Chromatin Immunoprecipitation, Methodological, Pricing, MYH-Associated Polyposis, CG3924, Methodological Study, LARGE_HUMAN, RABGAP5, plan specification, disease, MDC1D, cost, dLDB/Chip, like-glycosyltransferase, enr, multiple colorectal, MAP syndrome, inherited genetic, financial management, Cost Measure, hereditary, BEST, hypothesis, FAP2, glycosyltransferase-like protein LARGE1, Cost Analyses, colorectal adenomatous polyposis"],"pubmed_title_synonyms":["genetic, familial, microarray, anthropometry., inherited genetic, anthropometric traits, constitutitional genetic, hereditary"],"pubmed_abstract_synonyms":["Genome-Wide Association, Soluble, Adult-Onset Diabetes Mellitus, Diabetes Type 2, type 2, Insulin B Chain, scale tissue, Strokes, infarction (MI), determination, acetylglucosaminyltransferase-like protein, Whole Genome Association Study, Glukose, Blood, Mbp1, Monohydrate, Type 2 Diabetes Mellitus, insuline humaine, (DL)-Isomer, Measure, Coronary, CG30327, diabetes mellitus type 2, Cost-Minimization, CG11478, Readability, diseases, Body Mass, human insulin, Associations, Dextrose, Non-Insulin Dependent Diabetes Mellitus, Maturity Onset Diabetes, AW048865, diseases and disorders, Analysis, Systolic, Cost Comparison, myd, Slow Onset, Left Main Coronary Artery Disease, GWA Study, Cardiac infarction, DmelCG42257, insulin, human disease, Coronary Arteriosclerosis, Man (Taxonomy), like-acetylglucosaminyltransferase, Genomes, Analyses, myocardial infarction (disease), Cost-Minimization Analyses, plant peltate hair, Mbp-1, Comparison, DL-glucose, Genome-Wide Association Studies, Ketosis-Resistant Diabetes Mellitus, NIDDM, genetic, Stroke, glucose, Cost Analysis, Noninsulin-Dependent, insulin human, Diabetes mellitus, Quetelet, MODY (Maturity-onset diabetes of the young), Homo sapiens disease, Comparisons, Affordabilities, Non Insulin Dependent, Heart Attacks, Myocardial infarction, insulinum humanum, Left Main Coronary Disease, Infarct, Regular, wide/broad, Index, Myocardial Infarcts, gyltl1b-b, Infarcts, Adult-onset diabetes mellitus, frequency, Modern, familial, Myocardial Infarct, Genome-Wide, results, Noninsulin-dependent diabetes mellitus, Regular Insulin, Adult-Onset, insulin (recombinant), Genome Wide Association Study, Adult-Onset Diabetes, Cardiovascular Stroke, MDDGA6, CG6393, mKIAA0609, Myocardial infarction NOS, Quetelet's Index, Lipid, Diseases, NOS, Coronary Arterioscleroses, Ketosis Resistant, Whole Genome Association Analysis, (alpha-D)-Isomer, KIAA0609, Soluble Insulin, Maturity-Onset Diabetes Mellitus, finances, acetylglucosaminyltransferase-like 1A, fg, D-Glucose, heart attack, Dmel_CG6393, gyltl1b, follow up, mdc1d, Type II Diabetes, insulina humana, salaries, Atherosclerosis, whole genome, Type 2, surveillance, LARGE_HUMAN, MYOCARDIAL INFARCTION, morbidity, human, Noninsulin-Dependent Diabetes Mellitus, type II, MDC1D, disease, wide, myocardial, non-insulin-dependent, Non-Insulin Dependent Diabetes, Artery Disease, enr, D Glucose, Festa, Infarction of heart, Heart attack, microarray, inherited genetic, Association Study, (MI), financial management, Glucose Monohydrate, Slow-Onset, Infarction, Cost Analyses, T2DM - Type 2 Diabetes mellitus, gluco-hexose, lipids, Pulse Pressure, other disease, human being, FESTA-L, Glucose, FESTA-S, Noninsulin Dependent, Genome Wide Association Analysis, peltate hair, Traits., Cost Comparisons, Insulin B, broad, DIABETES MELLITUS TYPE 02, Diastolic Pressure, LARGE1, Maturity-onset diabetes, froggy, Gyltl1a, Human, Attack - heart, GWA Studies, Cost Minimization Analysis, Homo sapiens, Insulin, Non-Insulin-Dependent, Studies, disease or disorder, Arterioscleroses, Myocardial Infarction, non-insulin-dependent diabetes mellitus, Trait, Man, U19, Maturity-Onset Diabetes, Quetelet Index, T2DM, Chain, BM040, occurrence, Cost Measures, Coronary Atheroscleroses, MDDGB6, Non-Insulin-Dependent Diabetes Mellitus, Affordability, GWA, prevalence, Atheroscleroses, Coronary Artery Diseases, Measures, LARGE, Maturity Onset Diabetes Mellitus, financing, adult-onset, Solution, Genotypes, Genome Wide Association Scan, BMI, non-neoplastic, Study, funding, BPFD#36, Iletin, Maturity-onset diabetes mellitus, Noninsulin Dependent Diabetes Mellitus, Insulin recombinant, Stable, Diabetes Mellitus, 65K, Diastolic, CG42257, Dmel_CG30327, disorder, Ketosis-Resistant, Heart Attack, snp, constitutitional genetic, Diabetes, Anhydrous, incidence, Adult Onset, Type 2 diabetes, fees, cg11478, coronary arteriosclerosis, MI - Myocardial infarction, myocardial infarction, (beta-D)-Isomer, Adult-onset diabetes, Type 2 diabetes mellitus, Left Main Disease, Traits, MYOCARDIAL, disorders, MODY, medical condition, MI, myocardial infarct, T2D, Sodium Insulin, Genogroup, Pressure, chemical analysis, Insulin A Chain, Slow-Onset Diabetes Mellitus, Maturity-Onset, condition, Type 2 Diabetes Mellitus Non-Insulin Dependent, Sodium, Novolin, Arteriosclerosis, Left Main Diseases, scales, outbreaks, Costs and Cost Analyses, Costs, Cardiovascular, Type 2 Diabetes, Exubera, Systolic Pressure, scale, Myocardial Infarctions, Artery Diseases, Cost, Coronary Atherosclerosis, Cost-Minimization Analysis, Myocardial, Pricing, Understanding, TRAITS, endemics, Genome Wide Association Studies, Anhydrous Dextrose, Genogroups, cost, Quetelets Index, Pulse, Infarctions, Pressures, like-glycosyltransferase, Coronary Artery Disease, Modern Man, Association Studies, epidemics, INFARCTION (MI), assay, Type II, Cost Measure, Cardiovascular Strokes, hereditary, Stable Diabetes Mellitus, Maturity Onset, Myocardial infarction (disorder), glycosyltransferase-like protein LARGE1, Glc"],"additional_accession":[]},"is_claimable":false,"name":"Association 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)","description":"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).","dates":{"updated":"2019-10-31 12:52:09"},"accession":"EGAS00000000115","cross_references":{"TAXONOMY":["9606"],"pubmed":["22876189"],"EGA":["EGAD00010000232","EGAD00010000234","EGAD00010000230","EGAD00010000236","EGAC00001000205"]}}