This page provides information to enable researchers to access data (and other) resources from GWAS studies on type 1 diabetes. Please note that there are specifically designed data repositories for individual-level genotyping data from GWAS studies. T1DBase is not a repository for individual-level genotyping data.
Summary of genome wide resources available
|1||T1DGC||UK GRID||Illumina 550K||Illuminus||Case||~4K||Website||dbGAP|
|1958 Birth Cohort||Illumina 550K||Illuminus||Control||~2.5K||16155052||EGA|
|2||WTCCC||Type I Diabetes||Affy 500K||CHIAMO||Case||~2K||17554300||EGA|
|National Blood Service||Affy 500K||CHIAMO||Control||~1.5K||17554300|
|Bipolar Disorder||Affy 500K||CHIAMO||Control||~2K|
|1958 Birth Cohort||Affy 500K||CHIAMO||Control||~1.5K||16155052|
|WTCCC Retype||1958 Birth Cohort||Ilumina 550K||Illuminus||Control||~1.5K|
Note that the CCC inital and subsequent re-type of 1958 Birth Cohort contains the same subject set. The T1DGC typing of the 1958 BC for controls contains a different set of subjects to this.
For the T1DGC meta-analysis this gives approximately 7.8K cases and 7.3K controls (~1.5K are retyped).
Current GWAS studies in T1DBase.
|Description||Cohorts involved||Further information|
|WT CCC analysis||2||Replication 17554260|
|USA/CCC Meta analysis||2,3,4||18978792|
|T1DGC Meta analysis||1,2,3,4|
Type 1 Diabetes Genetics Consortium Cases
- The principal investigator along with an institution’s signing officer need to create an account on the NIH eRA commons system (If you have applied for grants through the NIH this should already be setup).
- On the dbGAP website click on login and enter the eRA username and password for the PI involved.
- A preference section will need to be filled in if this is the first request from dbGAP.
- Finally follow the links for the SF 424 R&R form for the study of choice. The information required is a statement summarising proposed research, and a list of collaborators at the same institution.
- Having submitted this form the signing officer for your institution will be notified automatically. A decision will be made by the relevant data access committe.
- On success the data will be made available to you through dbGAP. The system allows the selection of files, which it packages automatically for retrieval. Please note that packaged data is only available for download for a limited period of time.
If you have any problems downloading data please contact dbGAP help desk
Type 1 Diabetes Genetics Consortium Controls
T1DGC individual level information for controls is available by application to the 1958 Birth Cohort Interim Access Committee. This requires that an application form is filled in and a material transfer agreement is signed. These should be sent to:
1958 British Birth Cohort Secretariat
Department of Health Sciences
University of Leicester
Full details of the application process are available at: http://www.b58cgene.sgul.ac.uk/application.php these apply to data, as well as DNA samples, which is the site’s emphasis.
Wellcome Trust Case Control Data (WTCCC)
WTCCC datasets are available on application to the consortium data access committee. Instructions are below, but in summary you will need to submit an application form, this should be submitted electronically to firstname.lastname@example.org and signed a data access agreement , A hard copy of this needs to be submitted to the address outlined below. Applications can include collaborators, but each Institution must submit a signed Data Access Agreement. On approval access to the data is through the European Genotype Archve, where you should login to obtain data.
This information is sourced from here.
The Consortium Data Access Committee will accept applications for access to data at any time. Applications for access to the data should be submitted using the form “Application for Access to Genotype Data“.
The Consortium Data Access Committee will consider straightforward applications on a rolling basis and aim to provide a decision within 2 months of receipt. Applications which require further consideration will be referred to the next available Access Committee meeting for discussion. WTCCC access info & guidelines, ver 12, June08
You will be informed if you application has been referred and you should receive a decision within 2 weeks following the meeting at which your application is considered.
Applicants must address all questions on the form and include a reference list. Application forms will be returned if submitted with incomplete or unclear information.
Completed application forms should be submitted electronically to the following email address: email@example.com
Any queries regarding access procedures or completion of the forms should be sent to this address.
The application should be accompanied by a signed Data Access Agreement. This must include a signature from the Head of Institute or person with the appropriate institutional or administrative authority. 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
Successful applicants for access to data will be designated as an “Approved User” and will receive a username and password to enable access to the WTCCC database.
1958 Birth Cohort Retyped samples
This data is currently available from EGA and includes 1438 samples from the 1958 British Birth Cohort typed on the Illumina Infinium 550K. Application for this data is the same as for the main WTCCC dataset. This applies to data as well as DNA samples.
GAIN:GoKinD case data are available through dbGAP. For access please refer to the instructions available for the T1DGC(Case) data above.
National Institute Of Mental Health (NIMH)
These are available through the NIMH. To gain access to this control dataset, you must demonstrate certification as a qualified investigator by submitting :-
- A letter containing the name, mailing address, e-mail address, fax number, and telephone number of the principal investigator. This letter should be written on the letterhead of the sponsoring institution at which the research will be conducted.
- The curriculum vitae of the principal investigator and all co-investigators.
- A completed Distribution Agreement, including specification of the research project to be conducted and signatures of the principal investigator and an authorized representative of the recipient institution.
In a covering letter indicate that you are requesting access to the data as a qualified investigator . Data and biomaterials will not be provided until an original signed copy of the Distribution Agreement is received. Requested materials should be sent to:
Thomas Lehner, Ph.D., M.P.H.
Acting Director, Office of Human Genetics & Genomic Resources
Chief, Genetic Basis of Mental Disorders Program
National Institute of Mental Health
6001 Executive Blvd., Room 7190, MSC 9643
Bethesda, MD 20892-9643
Rockville, Maryland 20852 (for courier service)
There is an alternative mechanism to gain access by applying for peer-reviewed NIMH funding more details are available on NIMH website