ID
45609
Description
Principal Investigator: Jose Florez, Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA, and Massachusetts General Hospital, Boston, MA, USA MeSH: Diabetes Mellitus, Type 2 https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001375 The ~52,000 sample Type 2 Diabetes Exome Sequencing project is a collaboration of six consortia with various funding mechanisms that have joined together to investigate genetic variants for type 2 diabetes (T2D) using the largest T2D case/control sample set compiled to date. This includes samples from: - Type 2 Diabetes Genetic Exploration by Next-generation sequencing in multi-Ethnic Samples (T2D-GENES) - Genetics of Type 2 Diabetes (GoT2D) - Exome Sequencing Project (ESP) - Slim Initiative in Genomic Medicine for the Americas: Type 2 Diabetes (SIGMA T2D) - Lundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention, and Care (LuCAMP) - Progress in Diabetes Genetics in Youth (ProDIGY) This data generated from the SIGMA Mexico City Diabetes Study was part of the Slim Initiative in Genomic Medicine for the Americas: Type 2 Diabetes (SIGMA T2D), which is an international research consortium funded by the Carlos Slim Foundation that seeks to identify the genetic risk factors for type 2 diabetes (T2D) in Mexico and Latin America and translate those findings into improved treatment and prevention of diabetes. The SIGMA T2D project has sequenced and genotyped more than 13,000 samples from Mexican and Mexican Americans. The individuals were obtained from over 20 cohorts across the 6 consortia that are listed in Table 1. The strategy was to perform deep exome sequencing of individuals, 24,991 with T2D and 24,953 controls, divided among five ancestry groups: Europeans, East Asians, South Asians, American Hispanics, and African Americans. The T2D-GENES, ProDIGY and SIGMA studies, sequencing was performed at the Broad Institute using the Agilent v2 capture reagent or Illumina Rapid Capture on Illumina HiSeq machines. Please note that while we summarize the full sample list in publications and below, two of the cohorts below are not in dbGaP, due to the samples not being consented for deposition. This includes the Kooperative Gesundheitsforschung in der Region Augsburg (KORA) study and Lundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention, and Care (LuCamp) study. The Exome Sequencing Project (ESP) was deposited in dbGaP as part of their initial study and the phs numbers for that project can be found here: https://esp.gs.washington.edu/drupal/dbGaP_Releases table style="width:100%" border="1" captionTable 1. 52,000 sample T2D Case/Control Whole Exome Sequencing Studies/caption tbodytr thAncestry/th thConsortia/th thStudy/th thCountries of Origin/th th# Cases/th th# Controls/th /tr tr tdAfrican American/td tdT2D-GENES Project 1/td tdJackson Heart Study/td tdUS/td td500/td td526/td /tr tr tdAfrican American/td tdT2D-GENES Project 1/td tdWake Forest School of Medicine Study/td tdUS/td td518/td td530/td /tr tr tdAfrican American/td tdESP/td tdExome Sequencing Project (ESP)/td tdUS/td td467/td td1374/td /tr tr tdAfrican American/td tdT2D-GENES Follow up study/td tdBioMe Biobank Program (BioMe)/td tdUS/td td1297/td td1256/td /tr tr tdEast Asian/td tdT2D-GENES Project 1/td tdKorea Association Research Project/td tdKorea/td td526/td td561/td /tr tr tdEast Asian/td tdT2D-GENES Project 1& Follow up Study/td tdSingapore Diabetes Cohort Study; Singapore Prospective Study Program/td tdSingapore (Chinese)/td td1486/td td1568/td /tr tr tdEast Asian/td tdT2D-GENES Follow up study/td tdKorea SNUH/td tdSouth Korea/td td450/td td475/td /tr tr tdEast Asian/td tdT2D-GENES Follow up study/td tdResearch Studies in Hong Kong (Hong Kong)/td tdHong Kong/td td493/td td485/td /tr tr tdEuropean/td tdT2D-GENES Project 1/td tdAshkenazi/td tdUS, Israel/td td506/td td355/td /tr tr tdEuropean/td tdT2D-GENES Project 1/td tdMetabolic Syndrome in Men Study (METSIM)/td tdFinland/td td484/td td498/td /tr tr tdEuropean/td tdGoT2D/td tdFinland-United States Investigation of NIDDM Genetics (FUSION) Study/td tdFinland/td td472/td td476/td /tr tr tdEuropean/td tdGoT2D/td tdKooperative Gesundheitsforschung in der Region Augsburg (KORA)/td tdGermany/td td97/td td90/td /tr tr tdEuropean/td tdGoT2D/td tdUK Type 2 Diabetes Genetics Consortium (UKT2D)/td tdUK/td td322/td td320/td /tr tr tdEuropean/td tdGoT2D/td tdMalmo-Botnia Study/td tdFinland, Sweden/td td478/td td443/td /tr tr tdEuropean/td tdLuCamp/td tdLundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention, and Care (LuCamp)/td tdDenmark/td td997/td td997/td /tr tr tdEuropean/td tdESP/td tdExome Sequencing Project (ESP)/td tdUS/td td390/td td2843/td /tr tr tdEuropean/td tdT2D-GENES Follow up study/td tdGenetics of Diabetes and Audit Research Tayside Study (GoDARTS)/td tdScotland, UK/td td960/td td966/td /tr tr tdEuropean/td tdT2D-GENES Follow up study/td tdFramingham Heart Study (FHS)/td tdUS/td td396/td td596/td /tr tr tdHispanic/td tdT2D-GENES Project 1/td tdSan Antonio Family Heart Study, San Antonio Family Diabetes/ Gallbladder Study, Veterans Administration Genetic Epidemiology Study, and the Investigation of Nephropathy and Diabetes Study Family Component/td tdUS/td td272/td td218/td /tr tr tdHispanic/td tdT2D-GENES Project 1 & SIGMAv2/td tdStarr County, Texas/td tdUS/td td1762/td td1738/td /tr tr tdHispanic/td tdSIGMAv1/td tdMexico City Diabetes Study/td tdMexico/td td281/td td549/td /tr tr tdHispanic/td tdSIGMAv1 & v2/td tdMultiethnic Cohort (MEC)/td tdUS/td td1476/td td1443/td /tr tr tdHispanic/td tdSIGMAv1 & v2/td tdUNAM/INCMNSZ Diabetes Study (UIDS)/td tdMexico/td td1998/td td1977/td /tr tr tdHispanic/td tdSIGMAv1 & v2/td tdDiabetes in Mexico Study (DMS)/td tdMexico/td td1522/td td1546/td /tr tr tdMulti ethnic/td tdProDIGY/td tdTreatment Options for Type 2 Diabetes in Adolescents and Youth (TODAY)/td tdUS/td td3097/td td0/td /tr tr tdMulti ethnic/td tdProDIGY/td tdSEARCH for Diabetes in Youth (SEARCH)/td tdUS/td td553/td td0/td /tr tr tdSouth Asian/td tdT2D-GENES Project 1/td tdLondon Life Sciences Population Study (LOLIPOP)/td tdUK (Indian Asian)/td td531/td td538/td /tr tr tdSouth Asian/td tdT2D-GENES Project 1 & Follow up study/td tdSingapore Indian Eye Study/td tdSingapore (Indian Asian)/td td1640/td td1478/td /tr tr tdSouth Asian/td tdT2D-GENES Follow up study/td tdPakistan Genomic Resource (PGR)/td tdPakistan/td td914/td td932/td /tr /tbody/table
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- 2/21/23 2/21/23 - Chiara Middel
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Jose Florez, Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA, and Massachusetts General Hospital, Boston, MA, USA
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February 21, 2023
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dbGaP phs001375 Slim Initiative in Genomic Medicine for the Americas (SIGMA): Mexico City Diabetes Study (MCDS)
The subject consent file includes subject IDs, consent information, and subject aliases.
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent file includes subject IDs, consent information, and subject aliases.
- This data table contains a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs.
- This subject phenotype table contains subject IDs, sex, age, diabetes status, BMI, consortium name, ancestry name, cohort name, sample IDs, family IDs, c-peptide, c-peptide level post 2 hour glucose tolerance test, diastolic blood pressure, fasting glucose, fasting insulin, 2-hour glucose, glycated hemoglobin A1c, high-density lipoprotein, height, hip cicumference, homeostatic model assessment for beta cell function, insulin post 2 hour glucose tolerance test, low-density lipoprotein, leptin, systolic blood pressure, total cholesterol, triglycerides, ratio of triglyceride to high-density lipoprotein, waist circumference, waist to hip ratio, adiponectin, creatinine, homeostatic model assessment for insulin resistance, and medication for lipid levels.
- This sample attribute table contains sample IDs, body site from where sample was taken, analyte type, histological type, and name of the center which conducted sequencing.
Similar models
The subject consent file includes subject IDs, consent information, and subject aliases.
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent file includes subject IDs, consent information, and subject aliases.
- This data table contains a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs.
- This subject phenotype table contains subject IDs, sex, age, diabetes status, BMI, consortium name, ancestry name, cohort name, sample IDs, family IDs, c-peptide, c-peptide level post 2 hour glucose tolerance test, diastolic blood pressure, fasting glucose, fasting insulin, 2-hour glucose, glycated hemoglobin A1c, high-density lipoprotein, height, hip cicumference, homeostatic model assessment for beta cell function, insulin post 2 hour glucose tolerance test, low-density lipoprotein, leptin, systolic blood pressure, total cholesterol, triglycerides, ratio of triglyceride to high-density lipoprotein, waist circumference, waist to hip ratio, adiponectin, creatinine, homeostatic model assessment for insulin resistance, and medication for lipid levels.
- This sample attribute table contains sample IDs, body site from where sample was taken, analyte type, histological type, and name of the center which conducted sequencing.
C0441833 (UMLS CUI [1,2])
C0242481 (UMLS CUI [1,2])
C0449416 (UMLS CUI [1,2])
C3847505 (UMLS CUI [1,2])
C0449416 (UMLS CUI [1,3])