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- Study Description
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Important Links and Information
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- Instructions for requestors
- Data Use Certification (DUC) Agreement
- Talking Glossary of Genetic Terms
This is a genome-wide study of genetic associations with psoriatic arthritis (PsA), an inflammatory musculoskeletal condition that develops in up to 30% of people who have chronic psoriasis skin lesions. 1,526 cases affected with psoriatic arthritis and 1,508 unaffected controls were recruited and typed on the Illumina HumanOmni1-Quad BeadChip array. After application of quality control measures to both samples and SNPs, genotypes for 791,217 autosomal SNPs were available for 1,430 PsA cases and 1,417 controls. Imputation using phased haplotypes for the EUR subpopulation of release 3, phase 1 of the 1000 Genomes Project as a reference, resulted in genotypes for 11,532,644 SNPs and 918,976 indels passing our imputation quality threshold (Mach r2 ≥ 0.3) that were available for downstream analysis. Association at a genome-wide threshold of significance was found for five regions (near genes TNIP1, IL12B, HLA-C, TRAF3IP2, and TYK2).
- Study Weblinks:
- Study Design:
- Case-Control
- Study Type:
- Case-Control
- dbGaP estimated ancestry using GRAF-pop
- Total number of consented subjects: 2847
- Subject Sample Telemetry Report (SSTR)
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- Authorized Access
- Publicly Available Data
- Link to other NCBI resources related to this study
- Study Inclusion/Exclusion Criteria
Cases were all diagnosed by a rheumatologist as having psoriatic arthritis; most were evaluated using CASPAR criteria. Controls were at least 18 years of age and unaffected with either psoriasis or psoriatic arthritis. After genotyping on the Illumina array, we applied the usual quality controls measures to the samples. Samples were excluded if they represented a population outlier with substantial non-European admixture (determined with PCA), were duplicates or first or second degree relatives of other samples, had a genotype call rate < 98%, had outlier values for inbreeding coefficient ≥ 1.5 times the interquartile range beyond the lower or upper quartiles (F < -0.0225 or F > 0.0285), or were part of unresolvable sample swaps determined by X chromosome genotypes.
- Molecular Data
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Type Source Platform Number of Oligos/SNPs SNP Batch Id Comment Whole Genome Genotyping Illumina HumanOmni1-Quad BeadChip N/A N/A - Selected Publications
- Diseases/Traits Related to Study (MeSH terms)
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- Primary Phenotype: Arthritis, Psoriatic
- Links to Related Genes
- Authorized Data Access Requests
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See research articles citing use of the data from this study
- Study Attribution
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Principal Investigator
- James T. Elder. Department of Dermatology, University of Michigan, Ann Arbor, MI, USA.
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Funding Sources
- R01AR042742. National Institute for Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
- R01AR050511. National Institute for Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
- R01AR054966. National Institute for Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
- R01AR062382. National Institute for Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
- R01AR065187. National Institute for Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
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Principal Investigator