Progress in Diabetes Genetics in Youth (ProDIGY) Exome Sequencing Study: SEARCH for Diabetes in Youth

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 SEARCH for Diabetes in Youth cohort was part of the ProDIGY (Progress in Diabetes Genetics in Youth) consortium, which is a NIDDK-funded research consortium that investigated genetic variants for childhood type 2 diabetes (T2D). This consortium involved sequencing multiethnic samples from childhood T2D cases located across the United States.

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

The SEARCH study contributed 553 cases and 0 controls to 52k T2D exome sequencing study.

• Type: Case-Control
• Archiver: The database of Genotypes and Phenotypes (dbGaP)