Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Multi-Ethnic Samples (T2D-GENES) Follow-Up Study: Research Studies in Hong Kong

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 Hong Kong 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 500 526 African American T2D-GENES Project 1 Wake Forest School of Medicine Study US 518 530 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 506 352 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 Risk of Myocardial Infarction Study (PROMIS) Pakistan 914 932 The research studies in Hong Kong contributed 493 cases and 485 controls to T2D-GENES Follow-Up study.]]>
T2DM subjects were selected from the Hong Kong Diabetes Registry and Hong Kong Diabetes Family Study at CUHK. Priority for individuals with young onset DM. Controls were determined according to the following criteria: Controls were identified from a population based cohort of healthy adults in Hong Kong (Li Ka Shing cohort), together with another study which recruited healthy adults for clinical studies. ]]>
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. 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. 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. 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. Follow-Up study sought to understand the role of genetic variants in T2D risk and continue the work from Project 1, which is described in Fuchsberger et al. 2016. In order to get more power to assess variants, more samples were needed. The Follow-Up study selected an additional 15,334 T2D case and control samples to add to the existing data set. This submission reflects the activities that occurred in T2D-GENES Follow-Up study. Each of the studies involved in T2D-GENES Project1 and the T2D-GENES Follow-Up study 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 Exome Sequencing Study (Project 1 and Follow-Up Study) T2D-GENES Project Study Name PI(s) Study URL (if available) Project 1 Jackson Heart Study Candidate Gene Association Resource Jim Wilson Project 1 Wake Forest Study Donald Bowden Project 1 Korea Association Research Project (KARE) and Korean National Institute of Health (KNIH) Jong-Young Lee and Yoon Shin Cho Project 1 and Follow-Up Study Singapore Diabetes Cohort Study and Singapore Prospective Study Program Daniel Ng Peng Keat and Tai E. Shyong http://blog.nus.edu.sg/sphs/ Project 1 Longevity Genes in Founder Populations (Ashkenazi) Nir Barzilai, Gil Atzmon http://www.einstein.yu.edu/centers/aging/longevity-genes-project/ Project 1 Metabolic Syndrome in Men Study Markku Laakso http://www.nationalbiobanks.fi/index.php/studies2/10-metsim Project 1 San Antonio Mexican American Family Studies, Texas Ravindranath Duggirala Project 1 and Follow-Up Study Starr County, Texas Craig Hanis Project 1 London Life Sciences Population (LOLIPOP) Jaspal Kooner http://www.lolipopstudy.org/ Project 1 Singapore Indian Eye Study Wong Tien Yin www.seri.com.sg/key-programmes/singapore-epidemiology Follow-Up Study Korea Seoul National University Hospital Soo-Heon Kwak, Kyong Soo Park www.seri.com.sg/key-programmes/singapore-epidemiology-of-eye-diseases-seed/ Follow-Up Study Framingham Heart Study (FHS) James Meigs, Josee Dupuis www.framinghamheartstudy.org/ Follow-Up Study Research Studies in Hong Kong Juliana Chan, Ronald Ma Follow-Up Study The Pakistan Risk of Myocardial Infarction Study (PROMIS) Danish Saleheen www.cncdpk.com/the-pakistan-risk-of-myocardial-infarction-study-promis Follow-Up Study BioMe Biobank Program Ruth Loos http://icahn.mssm.edu/research/ipm/programs/biome Follow-Up Study Genetics of Diabetes and Audit Research Tayside Study (GoDARTS) Colin Palmer https://icaps-htn.org/cohorts/godarts/ ]]>