The dbGaP (http://ncbi.nlm.nih.gov/gap/) data repository was used as a source for population controls with GWAS genotype data. Given the prevalence of celiac disease in populations of European descent, the inclusion of population-based sampled controls was expected to result in a negligible reduction in power compared to an equal sized control sample of clinically defined unaffected controls[14]. Data from two studies in dbGaP were utilized because they had large numbers of controls with reported European or Caucasian ancestry that were genotyped using the same Illumina Human 660W Quad v.1A array platform used by CIDR to genotype the celiac disease cases and unaffected controls from the North American Celiac Disease Consortium described above. The NHGRI eMERGE study called “GWAS on Cataract and HLD in the PMRP” contributed genome-wide genotypes, age and sex data for 1343 control samples. The NHGRI GENEVA study called “NHGRI Genome-Wide Association Study of Venous Thrombosis (GWAS of VTE)” contributed genome-wide genotypes, age and sex data for an additional 1295 control samples. Detailed information about both of these studies can be found at the dbGaP website. The genotype data
