Genotyping and Quality Control Procedures for Vitiligo GWAS
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Corresponding Organization :
Other organizations : University of Colorado Denver, St George's, University of London, University of Florida, Royal Hallamshire Hospital, San Gallicano Hospital, Hôpital Saint-André, Ghent University Hospital, LumaMed (United States)
Protocol cited in 8 other protocols
Variable analysis
- Genotypes of patients with vitiligo for approximately 610,000 markers
- Genomewide association study
- Genotyping of the SNPs that showed genomewide significance (P<5×10^{-8}) or near significance in the genomewide association study
- All mitochondrial markers and Y-chromosome markers were excluded, leaving 579,146 SNPs that were present in both patients and controls in the genomewide association data set
- Genotyping of the SNPs was performed with the use of the Sequenom MassArray iPLEX genotyping system
- Imputed genotypes for rs12206499, which is related to major-histocompatibility-complex (MHC) class I molecules and for technical reasons could not be genotyped
- Genotyped several SNPs in the NLRP1 (NLR family, pyrin domain–containing 1 gene) region, which was previously shown to be associated with vitiligo
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