T1DGC: Genome-Wide Association Study in Type 1 Diabetes, 2008

Cases with Type 1 Diabetes (T1D) in the UK, were part of the Wellcome Trust Case Control Consortium (WTCCC) - http://www.wtccc.org.uk - that first reported in 2007: Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 447, 661-678. [PubMed: 17554300] In this genome-wide association study (GWAS), funded by the NIH and JDRF, and sponsored by the Type 1 Diabetes Genetics Consortium (T1DGC), we were able to extend the case and control groups used in the WTCCC, with the intention of performing a well-powered meta-analysis. The study is written up as: Barrett, J.C., Clayton, D.G., Concannon, P., Akolkar, B., Cooper, J.D., Erlich, H.A., Julier, C., Morahan, G., Nerup, J., Nierras, C., Plagnol, V., Pociot, F., Schuilenburg, H., Smyth, D.J., Stevens, H., Todd, J.A., Walker, N.M., Rich, S.S. and The Type 1 Diabetes Genetics Consortium Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nature Genetics, PMID: 19430480. Resources - data: * Case data from this study is deposited here (i.e. in dbGaP) * Control data from this experiment - with subjects from the 1958 British Birth Cohort - is deposited with the European Genotype Archive (EGA): http://www.ebi.ac.uk/ega/ from where the WTCCC data is also available. * A complete description of how to request all components of the meta-analysis is available at: http://www.t1dbase.org/page/PosterView/display/poster_id/324 * Additional genetic data on the same case subjects, including some HLA types, are available from the Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory (JDRF/WT-DIL): http://www-gene.cimr.cam.ac.uk/todd/ Resources - samples: Case and control DNA samples are also available: * Case DNA samples are available from the JDRF/WT-DIL, as above, and will be available from the NIDDK Genetics Repository at Rutgers: https://www.niddkrepository.org * Control DNA samples are available from the 1958 British Birth Cohort (aka National Child Development Study): http://www.cls.ioe.ac.uk/studies.asp?section=000100020003 Use restrictions: There are access limitations to both data and samples, in order to keep their use in line with subjects' consent.]]>
The Genetics of Type 1 Diabetes National Sample Collection ManualCONSENT FORM (Children under 16)CONSENT FORM (Adults)CONSENT FORM (parents on behalf of children)CHILDHOOD ONSET DIABETES Information leaflet for patientsCHILDHOOD ONSET DIABETES Information leaflet for children (12-16 years)CHILDHOOD ONSET DIABETES Information leaflet for children (5-11 years)CHILDHOOD ONSET DIABETES Information leaflet for parentsLetter of invitation to ParentsLetter of invitation to PatientsThe UK GRID Genetic Resource Investigating DiabetesThe Genetics of Type 1 Diabetes National DNA Collection Instructionsregion-codes.tabpostcodes-regions-map.tabThis analysis of association between genotype and T1D status was performed by Jeff Barrett, David Clayton and others as part of the meta-analysis reported in:
Barrett, J.C., Clayton, D.G., Concannon, P., Akolkar, B., Cooper, J.D., Erlich, H.A., Julier, C., Morahan, G., Nerup, J., Nierras, C., Plagnol, V., Pociot, F., Schuilenburg, H., Smyth, D.J., Stevens, H., Todd, J.A., Walker, N.M., Rich, S.S. and The Type 1 Diabetes Genetics Consortium Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nature Genetics, PMID: 19430480
The T1DGC-lead/NIDDK-sponsored project extended the T1D case-control
analysis performed as part of the -WTCCC - by adding (before exclusions) 4075 cases and 2604 controls from the same collections.The case groups are described at:

http://www.childhood-diabetes.org.uk/grid.shtml

and are type 1 diabetics; insulin dependent for at least 6 months;
diagnosed between the ages of 6 months and 16 years inclusive; and
resident in mainland UK. In this instance, we also omitted subjects:
who appeared previously in the WTCCC GWAS; lacked cell-lined DNA; not of self-reported white ethnicity; who were known to be related to other subjects in the study; who were known to be part of other (e.g. family)studies; with incomplete paperwork; or failed DNA QC.

The control groups are part of the 1958 British Birth Cohort:

http://www.cls.ioe.ac.uk/studies.asp?section=000100020003

As with the cases, in this instance, we omitted subjects: who appeared previously in the WTCCC GWAS; lacked cell-lined DNA; not of
self-reported white ethnicity; who were known to be related to other
subjects in the study; or failed DNA QC.

Genotyping was conducted by Illumina, Inc., San Diego, CA using the
Illumina HumanHap550v3 (550k) Infinium Beadchip, and project-managed by
Dr Julie Alapaz.

p-values reported relate to this novel GWAS case-control data, plus
(in order to give ~ 4k vs 4k samples in the association tests) the
WTCCC controls as retyped at Wellcome Trust Sanger Institute using the
Illumina 550k HumanHap550v1 beadchip.
]]>Cases in GRID:      http://www.childhood-diabetes.org.uk/grid.shtml are: type 1 diabetics insulin dependent for at least 6 months diagnosed between the ages of 6 months and 16 years inclusive resident in mainland UK In this instance, we also omitted subjects: who appeared previously in the WTCCC GWAS lacked cell-lined DNA not of self-reported white ethnicity (for want of controls) who were known to be related to other cases in the study who were known to be part of other (e.g. family) studies with incomplete paperwork failed DNA QC ]]>
Cases (and controls) have appeared in a series of studies since 2003. A complete list of publications is included below. A baseline description paper is being prepared.]]>