Type 1 Diabetes Genetics Consortium (T1DGC): Multi-Ethnic ImmunoChip Study
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ABSTRACT:
PROVIDER: PRJNA738974 | ENA |
REPOSITORIES: ENA
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Project description:Type 1 Diabetes Genetics Consortium (T1DGC): Multi-Ethnic ImmunoChip Study
| PRJNA738975 | ENA
Project description:Type 1 Diabetes Genetics Consortium (T1DGC) ImmunoChip Study
| PRJNA285005 | ENA
Project description:<p>The Type 1 Diabetes Genetics Consortium (T1DGC) was formed to address issues of limited sample size and consistency of phenotyping that had limited genetic investigations on risk of type 1 diabetes (T1D). The T1DGC first collected affected sib pair (ASP) families from four geographic networks (Asia-Pacific, Europe, North America, United Kingdom). In addition, T1D cases and controls were ascertained from existing and de novo collections. The T1DGC assembled 2,601 T1D ASP families and 69 Parent-T1D offspring trios, T1D cases from the UK Genetic Resource Investigating Diabetes (UKGRID, N=6,670), and controls from the British 1958 Birth Cohort (B58BC, N=6,523), the UK National Blood Services collection (NBS, N=2,893) and the NIHR Cambridge Biomedical Research Centre BioResource (CBR, N=2,846). All samples included in this series have reported or self-declared European ancestry. All DNA samples were collected after approval from relevant institutional research ethics committees. Genotyping was performed using a custom Illumina Infinium high-density genotyping array, ImmunoChip (Illumina, Inc; CA) according to manufacturer's protocols. The ImmunoChip was designed to densely genotype, using 1000 Genomes and any other available disease specific resequencing data, immune-mediated disease loci identified by common variant GWAS. The ImmunoChip Consortium selected 186 distinct loci containing markers meeting genome wide significance criteria (P<5x10-8) from twelve such diseases (autoimmune thyroid disease, ankylosing spondylitis, Crohn's disease, celiac disease, IgA deficiency, multiple sclerosis, primary biliary cirrhosis, psoriasis, rheumatoid arthritis, systemic lupus erythematosus, T1D and ulcerative colitis). All 1000 Genomes Project pilot phase CEU population variants (Sept 2009 release) within 0.1cM (HapMap3 CEU) recombination blocks around each GWAS region lead marker were submitted for array design. No filtering on correlated variants (linkage disequilibrium) was applied. Additional content included regional resequencing data (submitted by several groups) as well as a small proportion of investigator-specific undisclosed content including intermediate GWAS results. After data cleaning and quality control, a total of 154,939 single nucleotide polymorphisms (SNPs) from 186 loci on ImmunoChip were scored. Case-control and family data were analyzed independently and combined by meta-analysis.</p>
| phs000911 | dbGaP
Project description:Type 1 Diabetes Genetics Consortium (T1DGC) ImmunoChip Study
| PRJNA283016 | ENA
Project description:<p>Peripheral blood mononuclear cells (PBMC) from 82 T1D cases from the T1DGC study were fractionated by positive selection on magnetic beads into CD4+ T cells, CD8+ T cells and CD19+ B cells. RNA purification, library preparation and sequencing to an average of 50 million reads per sample were performed by the HudsonAlpha Genome Services Laboratory. The resulting dataset includes 82 subjects with data from at least one cell type; sequence data from all 3 cell types is available from 79 subjects. The individuals in this study can be linked to the <a href="./study.cgi?study_id=phs000911">phs000911 T1DGC ImmunoChip</a> study via subject ids to obtain both genotypic and phenotypic information, including genotypes used for expression quantitative trait locus analysis.</p>
| phs001426 | dbGaP
Project description:Myocardial Genetics Exome Sequencing Consortium
| PRJNA262455 | ENA
Project description:<p>Cases with Type 1 Diabetes (T1D) in the UK, were part of the Wellcome Trust Case Control Consortium (WTCCC) - <a href="http://www.wtccc.org.uk" target="_blank">http://www.wtccc.org.uk</a> - that first reported in 2007:</p> <p>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: <a href="http://www.ncbi.nlm.nih.gov/pubmed/17554300" target="_blank">17554300</a>]</p> <p>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.</p> <p>The study is written up as:</p> <p>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: <a href="http://www.ncbi.nlm.nih.gov/pubmed/19430480" target="_blank">19430480</a>.</p> <p>Resources - data:</p> <p>* Case data from this study is deposited here (i.e. in dbGaP)</p> <p>* Control data from this experiment - with subjects from the 1958 British Birth Cohort - is deposited with the European Genotype Archive (EGA):</p> <p><a href="http://www.ebi.ac.uk/ega/" target="_blank">http://www.ebi.ac.uk/ega/</a></p> <p>from where the WTCCC data is also available.</p> <p>* A complete description of how to request all components of the meta-analysis is available at:</p> <p><a href="http://www.t1dbase.org/page/PosterView/display/poster_id/324" target="_blank">http://www.t1dbase.org/page/PosterView/display/poster_id/324</a></p> <p>* 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):</p> <p><a href="http://www-gene.cimr.cam.ac.uk/todd/" target="_blank">http://www-gene.cimr.cam.ac.uk/todd/</a></p> <p>Resources - samples:</p> <p>Case and control DNA samples are also available:</p> <p>* Case DNA samples are available from the JDRF/WT-DIL, as above, and will be available from the NIDDK Genetics Repository at Rutgers:</p> <p><a href="https://www.niddkrepository.org" target="_blank">https://www.niddkrepository.org</a></p> <p>* Control DNA samples are available from the 1958 British Birth Cohort (aka National Child Development Study):</p> <p><a href="http://www.cls.ioe.ac.uk/studies.asp?section=000100020003" target="_blank">http://www.cls.ioe.ac.uk/studies.asp?section=000100020003</a></p> <p>Use restrictions:</p> <p>There are access limitations to both data and samples, in order to keep their use in line with subjects' consent.</p>
| phs000180.v2.p2 | EGA
Project description:We aimed to exemplify early and late transcriptional response of M. galloprovincialis to live Vibrio cells. Hemolymph was collected at 3 and 48 hours after the injection of 10 to 7 cells Vibrio splendidus LGP32 into the posterior adductor muscle. Hemolymph samples were similarly collected from paired control mussels injected with PBS-NaCl. The purified RNAs were successfully amplified, labelled and competitively hybridized to the new mussel oligoarray Immunochip 1.0. After acclimatization, groups of 40 farmed mussels from the Venice lagoon (Italy) were injected either with 10 to 7 cells of Vibrio splendidus LGP32 or with NaCl-enriched PBS. One ml of hemolymph was withdrawn at 3 h and 48 h post-injection from each control or treated mussel. Two RNA pools (N=10) per time point were composed from the treated mussels, processed and competitively hybridized in dye-swap combination (Cy3 / Cy5 aRNAs) on the same Immunochip slide against time-paired control RNA pools (N=40). Since each Immunochip array contains 4 replicates per probe, the dye-swap testing yielded a total of 16 expression values per probe per time-point.
2011-04-12 | E-GEOD-23535 | biostudies-arrayexpress
Project description:<p>Type 1 Diabetes Genetics Consortium (T1DGC) was formed to address issues of limited sample size and consistency of phenotyping that had limited genetic investigations on risk of type 1 diabetes (T1D). The T1DGC first collected affected sib pair (ASP) families from four geographic networks (Asia-Pacific, Europe, North America, United Kingdom). In addition, T1D parent-offspring trios as well as cases and controls were ascertained from existing and de novo collections. For T1D, the genome-wide association study (GWAS) design has been successful at detecting ~50 loci that contribute disease risk. However, in the case of T1D as well as almost all other traits, the sum of these loci does not fully explain the heritability estimated from familial studies. One possibility for the undiscovered contribution to familial aggregation is that additional variants exist but have not yet been found because they have not effectively been targeted by the GWAS design. In this study, we focus on a specific class of large deletions/duplications -- copy number variants (CNVs) - and particularly to the subset of these loci that mutate rapidly, are not tagged by SNPs, and are highly polymorphic. The T1DGC assembled 2,601 T1D ASP families and 69 Parent-T1D offspring trios, that were eligible for this study. All samples included in this series have reported or self-declared European ancestry. All DNA samples were collected after approval from relevant institutional research ethics committees. Importantly, the source of DNA for CNV evaluation was uniform within a family (either all from PBMC or from EBV-transformed cell lines). We use a family based design that was optimized to capture these previously untested variants. We then perform a genome-wide scan to assess their contribution to T1D.</p>
| phs000910 | dbGaP