ID
45991
Description
Principal Investigator: Stephen S. Rich, PhD, University of Virginia, Charlottesville, VA, USA MeSH: Diabetes Mellitus, Type 1,Autoimmune Diseases,Autoantibodies https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000911 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 (P5x10-8) 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.
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- 4/11/24 4/11/24 - Madita Rudolph
Copyright Holder
Stephen S. Rich, PhD, University of Virginia, Charlottesville, VA, USA
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April 11, 2024
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Creative Commons BY 4.0
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dbGaP phs000911 Type 1 Diabetes Genetics Consortium (T1DGC): ImmunoChip Study
This subject sample mapping data table includes a mapping of study subject IDs to sample IDs, both of which are T1DGC Analytic IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes sample use.
- StudyEvent: SEV1
- Eligibility Criteria
- This subject consent data table includes subjects IDs (T1DGC Analytic ID), consent information, T1D affection status, and mapping to subject aliases.
- This pedigree data table contains family relationships in the format of family IDs, subject IDs, father IDs, mother IDs, sex of subjects, and twin IDs.
- This subject sample mapping data table includes a mapping of study subject IDs to sample IDs, both of which are T1DGC Analytic IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes sample use.
- This subject phenotype data table for affected sib pair (ASP) families includes sex of the participant, age at ascertainment, and best sample type.
- This subject phenotype data table for UK Genetic Resource Investigating Diabetes (UKGRID) includes type 1 diabetes (T1D) status, sex of the participant, approximate year of birth, region of the UK developed by the 1958 British Birth Cohort, self-reported ethnicity, and best sample type.
- This sample attributes data table includes body site where sample was collected, DNA source, analyte type, tumor status, and genotyping center.
Similar models
This subject sample mapping data table includes a mapping of study subject IDs to sample IDs, both of which are T1DGC Analytic IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes sample use.
- StudyEvent: SEV1
- Eligibility Criteria
- This subject consent data table includes subjects IDs (T1DGC Analytic ID), consent information, T1D affection status, and mapping to subject aliases.
- This pedigree data table contains family relationships in the format of family IDs, subject IDs, father IDs, mother IDs, sex of subjects, and twin IDs.
- This subject sample mapping data table includes a mapping of study subject IDs to sample IDs, both of which are T1DGC Analytic IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes sample use.
- This subject phenotype data table for affected sib pair (ASP) families includes sex of the participant, age at ascertainment, and best sample type.
- This subject phenotype data table for UK Genetic Resource Investigating Diabetes (UKGRID) includes type 1 diabetes (T1D) status, sex of the participant, approximate year of birth, region of the UK developed by the 1958 British Birth Cohort, self-reported ethnicity, and best sample type.
- This sample attributes data table includes body site where sample was collected, DNA source, analyte type, tumor status, and genotyping center.
C0042153 (UMLS CUI [1,2])
C0752046 (UMLS CUI [1,3])
C1449575 (UMLS CUI [1,4])
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