ID
45990
Descrizione
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=phs000910 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.
collegamento
Keywords
versioni (1)
- 2024-04-11 2024-04-11 - Madita Rudolph
Titolare del copyright
Stephen S. Rich, PhD, University of Virginia, Charlottesville, VA, USA
Caricato su
11 april 2024
DOI
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Licenza
Creative Commons BY 4.0
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dbGaP phs000910 Type 1 Diabetes Genetics Consortium (T1DGC): Copy Number Variant (CNV) Study
This sample attributes data table includes DNA source and shipment date, OGT scan date, OGT hybridization oven and processbatch, ACGH slide barcode, location, and processing date, hybridization barcode and position, mother plate and position, and sample swap information.
- StudyEvent: SEV1
- Eligibility Criteria
- This subject consent data table includes subjects IDs, consent information, T1D affection status, and mapping to subject aliases.
- This pedigree data table shows family relationships through family IDs, subject IDs, father IDs, mother IDs, sex, and family membership codes.
- This subject sample mapping data table includes a mapping of study subject IDs to sample 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 aliases and sample use.
- This subject phenotype data table contains gender of participant, T1DGC collection information, T1D status, disease onset age, and age at sampling.
- This sample attributes data table includes DNA source and shipment date, OGT scan date, OGT hybridization oven and processbatch, ACGH slide barcode, location, and processing date, hybridization barcode and position, mother plate and position, and sample swap information.
Similar models
This sample attributes data table includes DNA source and shipment date, OGT scan date, OGT hybridization oven and processbatch, ACGH slide barcode, location, and processing date, hybridization barcode and position, mother plate and position, and sample swap information.
- StudyEvent: SEV1
- Eligibility Criteria
- This subject consent data table includes subjects IDs, consent information, T1D affection status, and mapping to subject aliases.
- This pedigree data table shows family relationships through family IDs, subject IDs, father IDs, mother IDs, sex, and family membership codes.
- This subject sample mapping data table includes a mapping of study subject IDs to sample 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 aliases and sample use.
- This subject phenotype data table contains gender of participant, T1DGC collection information, T1D status, disease onset age, and age at sampling.
- This sample attributes data table includes DNA source and shipment date, OGT scan date, OGT hybridization oven and processbatch, ACGH slide barcode, location, and processing date, hybridization barcode and position, mother plate and position, and sample swap information.
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