Access to WTCCC genotype data and samples

The primary purpose of the WTCCC is to accelerate efforts to identify genome sequence variants influencing major causes of human morbidity and mortality, through implementation and analysis of large-scale genome wide association studies. Additional objectives include the development and validation of informatics and analytical solutions appropriate to the scale and nature of the project, as well as use of the data generated to answer important methodological and biological questions relevant to association studies in general, and in the UK in particular (for example issues of population substructure).

The Consortium anticipates that data generated from the project will be used by others, such as required for developing new analytical methods, in understanding patterns of polymorphism and in guiding selection of markers to map genes involved in specific diseases.

Summary genotype data for the collections listed below is available directly from the WTCCC website.

Access to individual-level genotype data is available by application to the Wellcome Trust Case Control Consortium Data Access Committee. Access to data will be granted to qualified investigators for appropriate use.

Data available

1. Data are available on the following samples using the 500K Affymetrix chip:

   • 1,500 samples from the 1958 British Birth Cohort
   • 1,500 samples from the UK Blood Service Control Group
   • 2,000 samples each from the following disease collections: type 1 diabetes, type 2 diabetes, rheumatoid arthritis, inflammatory bowel disease, bipolar disorder, hypertension, coronary artery disease.

   Two sets of genotypes are available for each of these, called by different algorithms: Chiamo as discussed and used in the analysis for the WTCCC papers and the Affymetrix algorithm BRLMM.

2. Data are available on the following samples using a custom Illumina chip with 15K non synonymous SNPs:

   • 1,500 samples from the 1958 British Birth Cohort
   • 1,000 samples each from the following disease collections: multiple sclerosis, autoimmune thyroid disease, ankylosing spondylitis and breast cancer.

   Genotypes from these samples were called with the Illumina algorithm GenCall.

How to apply

Please refer to the Information and Guidelines [DOC | PDF] for further information and for details on how to apply for access to the data.

An Application Form for access to the data should be completed and returned to cdac@wellcome.ac.uk. Any queries regarding access procedures or completion of the forms should be sent to this address.

Access to the data will require the completion of a Data Access Agreement [DOC | PDF]. Applications can include collaborators, but each Institution must submit a signed Data Access Agreement. A signed hard copy of the agreement should be posted or faxed to:

Dr A. Duncanson
Molecules, Genes and Cells
The Wellcome Trust
215 Euston Road
London NW1 2BE
Fax: 020 7611 8352