Type 2 Diabetes Genetic Exploration by Next-generation Sequencing in Multi-Ethnic Samples (T2D-GENES) Follow up Study: Pakistan Genomic Resource (PGR)
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 (SIGMA)
- 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 Pakistan Genomic Resource (PGR) cohort was part of the T2-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 | 1297 | 1256 |
| 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 | 903 | 930 |
The PGR study contributed 903 cases and 930 controls to T2D-GENES Follow-Up Study.
- Type: Case-Control
- Archiver: The database of Genotypes and Phenotypes (dbGaP)