A sample of 1728 celiac disease cases and 3168 control individuals were genotyped with the Illumina Human660W-Quad SNP genotyping array for the GWAS. After extensive quality control assessments of the SNPs and samples followed by appropriate filtering, a set of 517,345 SNPs was analyzed in a sample of 1550 cases and 3084 controls. Genome-wide statistical significance was defined as a p-value for the association statistic of less than 1.0×10−7. SNPs showing p-values between 1.0×10−6 and 1.0×10−7 were labeled as having suggestive evidence for association. The SNP association results from the previous celiac disease GWAS and follow-up studies of Dubois et al [7] were used to test for replication of the significant and suggestive findings found in the current GWAS. This replication set included 3,796 cases and 8,154 controls; the samples genotyped on the Hap550 platform described in Dubois et al. [7].
