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Study Description

T2D-GENES (Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Multi-Ethnic Samples) is a NIDDK-funded international research consortium which seeks to identify genetic variants for type 2 diabetes (T2D) through multiethnic sequencing studies. T2D-GENES Project 1 is a multi-ethnic sequencing study designed to assess whether less common variants play a role in T2D risk and to assess similarities and differences in the distribution of T2D risk variants across ancestry groups.

The individuals were obtained from 14 cohorts that are listed in Table 1. The strategy was to perform deep exome sequencing of 12,940 individuals, 6,504 with T2D and 6,436 controls, divided among five ancestry groups: Europeans, East Asians, South Asians, American Hispanics, and African Americans. Sequencing was performed at the Broad Institute using the Agilent v2 capture reagent on Illumina HiSeq machines. Please note that while we summarize the full sample list in publications and below, the Kooperative Gesundheitsforschung in der Region Augsburg (KORA) study does not have a sub study, as it is not consented to be deposited in dbGAP.

Table 1. T2D-GENES Whole Exome Sequencing Studies

Ancestry Study Countries of Origin # Cases # Controls
African American Jackson Heart Study US 502 527
African American Wake Forest School of Medicine Study US 518 532
East Asian Korea Association Research Project Korea 526 561
East Asian Singapore Diabetes Cohort Study; Singapore Prospective Study Program Singapore (Chinese) 486 592
European Ashkenazi US, Israel 506 352
European Metabolic Syndrome in Men Study (METSIM) Finland 484 498
European Finland-United States Investigation of NIDDM Genetics (FUSION) Study Finland 472 476
European Kooperative Gesundheitsforschung in der Region Augsburg (KORA) Germany 97 90
European UK Type 2 Diabetes Genetics Consortium (UKT2D) UK 322 320
European Malmö-Botnia Study Finland, Sweden 478 443
Hispanic San 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 US 272 219
Hispanic Starr County, Texas US 749 704
South Asian London Life Sciences Population Study (LOLIPOP) UK (Indian Asian) 530 538
South Asian Singapore Indian Eye Study Singapore (Indian Asian) 563 585

The Metabolic Syndrome in Men Study (METSIM) contributed 484 cases and 498 controls to T2D-GENES Project 1.

  • Study Weblinks:
  • Study Design:
    • Case-Control
  • Study Type:
    • Case-Control
  • dbGaP estimated ancestry using GRAF-pop
  • Number of study subjects that have individual-level data available through Authorized Access:
Authorized Access
Publicly Available Data (Public ftp)

Note: Access to publicly available data is available on the public ftp site for study phs000743.v1.p1

Study Inclusion/Exclusion Criteria
Cases were ascertained according to the following criteria:
  • Previous diagnosis of T2D, or both fasting and 2-hr criteria met for new T2D diagnosis.
  • C-peptide >0.10 nmol/L.
  • Anti-GAD antibody <50 U/mL to rule out T1D.
  • Family history of diabetes (parents, sibs, children, grandparents, avuncular, cousins).
  • Unrelated individuals based on family ID and IBS analyses.
  • Preferentially select individuals with genotype data (N=494), as well as non-genotyped individuals with earlier possible age of diagnosis (N=26).

Controls were determined according to the following criteria:
  • Normal glucose tolerance at baseline and follow-up visits.
  • Prioritized samples with no family history of diabetes and meeting strict NGT criteria: fasting glucose <5.6 mmol/l and 2 hour post-challenge glucose <7.8 mmol/l.
  • Additional samples selected with fasting glucose <6.1 mmol/l and 2 hour post-challenge glucose <7.8 mmol/l.
  • Unrelated samples.
  • Older controls preferentially selected.
Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
Whole Exome Sequencing Agilent SureSelect Human All Exon v2 - 44Mb N/A N/A
Study History

T2D-GENES (Type 2 Diabetes Genetic Exploration by Next-generation Sequencing in Multi-Ethnic Samples) is a NIDDK-funded international research consortium which seeks to identify genetic variants for type 2 diabetes (T2D) through multiethnic sequencing studies. The organizations involved in the NIDDK U01 include: Broad Institute, University of Michigan, University of Oxford, NIDDK/NIH, University of Chicago, Texas Biomedical Research Institute, Massachusetts General Hospital, University of Texas Health Science Center, University of North Carolina, Blood Systems Research Institute, and University of Mississippi Medical Center.

The T2D-GENES collaboration effort consists of 3 projects:

  1. Project 1 seeks to assess whether less common variants play a role in T2D risk and to assess similarities and differences in the distribution of T2D risk variants across ancestry groups.
  2. Project 2 is focused on the role of rare and private variants on T2D risk, and is based on deep whole genome sequencing of ~600 members of 20 Mexican American pedigrees. Pedigree members are extensively phenotyped and have been genotyped with Illumina GWAS chips.
  3. Project 3 seeks to determine whether multiethnic GWAS meta-analysis might assist in fine-mapping T2D association signals by strengthening evidence for T2D association and narrowing the association interval. Project 3 has focused initially on analysis of five T2D loci chosen as likely candidates for success of this approach.

This submission reflects the activities that occurred in T2D-GENES Project 1. Each of the studies involved in T2D-GENES Project1 are part of larger cohorts. While each participating cohort has specific cohort information and history, that information is not summarized here as we have specifically selected these samples for type 2 diabetes research as part of the T2D-GENES study. For more information on these studies, please see table 2.

Table 2. Studies contributing samples to T2D-GENES Project 1

Study Name PI(s) Study URL (if available)
Jackson Heart Study Candidate Gene Association Resource Jim Wilson http://www.jacksonheartstudy.org
Wake Forest Study Donald Bowden
Korea Association Research Project (KARE) and Korean National Institute of Health (KNIH) Jong-Young Lee and Yoon Shin Cho
Singapore Diabetes Cohort Study and Singapore Prospective Study Program Daniel Ng Peng Keat and Tai E. Shyong http://www.nus-cme.org.sg/about.html
Longevity Genes in Founder Populations (Ashkenazi) Nir Barzilai, Gil Atzmon http://www.einstein.yu.edu/centers/aging/longevity-genes-project/
Metabolic Syndrome in Men Study Markku Laakso http://www.nationalbiobanks.fi/index.php/studies2/10-metsim
San Antonio Mexican American Family Studies, Texas Ravindranath Duggirala
Starr County, Texas Craig Hanis
London Life Sciences Population (LOLIPOP) Jaspal Kooner http://www.lolipopstudy.org/
Singapore Indian Eye Study Wong Tien Yin http://www.seri.com.sg/key-programmes/singapore-epidemiology-of-eye-diseases-seed/

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