The Genetic Association Information Network (GAIN)21 supported a series of Genome-Wide Association Studies (GWAS) designed to identify specific points of DNA variation associated with the occurrence of a particular common disease. Data used for this study included 1,359 psoriasis cases and 1,400 controls genotyped at Perlegen Sciences using a custom genotyping array. In total, 438,670 autosomal SNPs passed the quality control filters (HWE P ≥ 10−6 in the total sample, call frequency ≥ 0.95 and MAF > 0.01)21. In this study, 88 individuals were also genotyped using Affymetrix 6.0 arrays and these genotypes were used to evaluate imputation accuracy by examining the correlation between imputed dosages and array genotypes (for markers that were present on the Affymetrix 6.0 arrays but not on the Perlegen custom array).
