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Study Description

The Genetics of Type 2 Diabetes Consortium (GoT2D) is a collaboration between the University of Michigan, the Broad Institute and the Wellcome Trust Centre for Human Genetics. The overall aim is to extend upon recent efforts, such as genome-wide association studies (GWAS) and large scale meta-analyses. While they have proved successful at mapping genomic loci that influence human diseases, like type 2 diabetes, much of the heritability remains unexplained. In this study, we use next generation sequencing and genotyping technologies to query for lower frequency variants in the human genome. Thereby, allowing a deeper characterization of the spectrum of alleles associated with type 2 diabetes risk, and a better assessment of the genes that play a role in the etiology of type 2 diabetes development. We studied 1,326 T2D cases and 1,331 normoglycemic controls from Northern and Central Europe (Sweden, Finland, UK, and Germany). To efficiently characterize the entire genome sequence of each individual, we performed low-coverage (~5x) whole-genome sequencing, augmented by deep coverage (~100x) sequencing of the exome (Fuchsberger et al, 2016), and dense (2.5M) single nucleotide polymorphism (SNP) genotyping using the HumanOmni2.5 array. The data deposited in dbGaP will include all the Swedish, Finnish, and UK samples, but the German data will be deposited in the European Genome-phenome Archive (EGA), by virtue of the project specific funding requirements.

  • Study Weblink: T2D-GENES
  • Study Type: Case-Control
  • dbGaP estimated ancestry components using GRAF-pop
  • Number of study subjects that have individual level data available through Authorized Access: 2348

Authorized Access
Publicly Available Data (Public ftp)

Connect to the public download site. The site contains release notes and manifests. If available, the site also contains data dictionaries, variable summaries, documents, and truncated analyses.

Study Inclusion/Exclusion Criteria

We selected 1425 type 2 diabetes (T2D) and 1425 normoglycemic controls from Northern and Central Europe (2,000 from Sweden and Finland, 650 from the UK, and 200 from Germany). Controls were defined to be of normal glucose tolerance. We preferentially sampled early onset, lean, and/or familial T2D cases and overweight controls with low fasting glucose levels. After quality control filters, we studied for analysis, cases 1,171 T2D cases and 1,177 normoglycemic controls.

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
Whole Genome Genotyping Illumina HumanOmni2.5-8 (Omni2.5) 2379855 N/A
Whole Exome Sequencing Agilent SureSelect Human All Exon v2 - 44Mb N/A N/A
Whole Genome Sequencing Illumina Genome Analyzer II N/A N/A
Whole Genome Sequencing Illumina HiSeq 2000 N/A N/A
Whole Genome Sequencing Sage Science Pippin Prep N/A N/A
Selected publications
Diseases/Traits Related to Study (MESH terms)
Links to Related Resources
Authorized Data Access Requests
Study Attribution