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Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Multi-Ethnic Samples (T2D-GENES) Follow-Up Study: BioMe Biobank Program

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:

This data generated from the BioMe Biobank cohort was part of the T2D-GENES (Type 2 Diabetes Genetic Exploration by Next-generation sequencing in multi-Ethnic Samples) consortium, which is a NIDDK-funded international research consortium that seeks to identify genetic variants for type 2 diabetes (T2D) through multiethnic sequencing studies. The T2D-GENES Project 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 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 1. 52,000 sample T2D Case/Control Whole Exome Sequencing Studies

Ancestry Consortia Study Countries of Origin # Cases # Controls
African American T2D-GENES Project 1 Jackson Heart Study US 502 527
African American T2D-GENES Project 1 Wake Forest School of Medicine Study US 518 532
African American ESP Exome Sequencing Project (ESP) US 467 1374
African American T2D-GENES Follow-Up Study BioMe Biobank Program (BioMe) US 1294 1254
East Asian T2D-GENES Project 1 Korea Association Research Project Korea 526 561
East Asian T2D-GENES Project 1 and Follow-Up Study Singapore Diabetes Cohort Study; Singapore Prospective Study Program Singapore (Chinese) 1486 1568
East Asian T2D-GENES Follow-Up Study Korea SNUH South Korea 450 475
East Asian T2D-GENES Follow-Up Study Research Studies in Hong Kong (Hong Kong) Hong Kong 493 485
European T2D-GENES Project 1 Ashkenazi US, Israel 506 355
European T2D-GENES Project 1 Metabolic Syndrome in Men Study (METSIM) Finland 484 498
European GoT2D Finland-United States Investigation of NIDDM Genetics (FUSION) Study Finland 472 476
European GoT2D Kooperative Gesundheitsforschung in der Region Augsburg (KORA) Germany 97 90
European GoT2D UK Type 2 Diabetes Genetics Consortium (UKT2D) UK 322 320
European GoT2D Malmö-Botnia Study Finland, Sweden 478 443
European LuCamp Lundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention, and Care (LuCamp) Denmark 997 997
European ESP Exome Sequencing Project (ESP) US 390 2843
European T2D-GENES Follow-Up Study Genetics of Diabetes and Audit Research Tayside Study (GoDARTS) Scotland, UK 960 966
European T2D-GENES Follow-Up Study Framingham Heart Study (FHS) US 396 596
Hispanic T2D-GENES Project 1 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 272 218
Hispanic T2D-GENES Project 1 and SIGMA v2 Starr County, Texas US 1762 1738
Hispanic SIGMA v1 Mexico City Diabetes Study Mexico 281 549
Hispanic SIGMA v1 and SIGMA v2 Multiethnic Cohort (MEC) US 1476 1443
Hispanic SIGMA v1 and SIGMA v2 UNAM/INCMNSZ Diabetes Study (UIDS) Mexico 1998 1977
Hispanic SIGMA v1 and SIGMA v2 Diabetes in Mexico Study (DMS) Mexico 1522 1546
Multiethnic ProDIGY Treatment Options for Type 2 Diabetes in Adolescents and Youth (TODAY) US 3097 0
Multiethnic ProDIGY SEARCH for Diabetes in Youth (SEARCH) US 553 0
South Asian T2D-GENES Project 1 London Life Sciences Population Study (LOLIPOP) UK (Indian Asian) 531 538
South Asian T2D-GENES Project 1 and Follow-Up Study Singapore Indian Eye Study Singapore (Indian Asian) 1640 1478
South Asian T2D-GENES Follow-Up Study Pakistan Genomic Resource (PGR) Pakistan 914 932

The BioMe Biobank study contributed 1294 cases and 1254 controls to T2D-GENES Follow-Up Study.