Center for Inherited Disease Research (CIDR) completed the GWAS genotyping of 1728 celiac disease cases and 530 controls collected in the U.S. (funded by NIH R01 DK081645). The following quality control assessments and corrections were taken prior to the association analysis. All SNPs and samples with less than 98% complete data were excluded from the analysis. SNPs with allele frequencies less than 0.03 or genotype distributions that failed to fit the Hardy-Weinberg equilibrium (HWE) model with a p-value less than 1.0×10−5 were filtered from the data. The genotype data were used to test for unknown familial relationships between subjects by analysis of the identity-by-state distribution of the sample, misspecification of sex by analysis of chromosome X/Y genotypes, and population substructure among the subjects by multidimensional scaling of the computed identity-by-state matrix and cluster analysis of the samples. Population genetic outliers identified in the population substructure analysis were excluded from the subsequent association analysis. Exclusions were made when discrepancies could not be resolved. The GenABEL library [15] of R statistical computing environment was used for the quality control assessments.
