Meta-analysis of six Crohn’s disease genomewide association studies (GWAS) comprising 6,333 affected individuals (cases) and 15,056 controls of european descent. Genotyping in the six studies was performed on Illumina and Affymetrix platforms. Imputation was done with the BEAGLE software using Hapmap 3 for 5 studies and with the MACH software using Hapmap 2 for 1 study (early-onset). 953,241 SNPs were available for analysis. 51 SNPs were selected for replication in 15,694 cases, 14,026 controls and 414 parent-offspring trios. In total 39 new Crohn’s disease susceptibility loci were confirmed.
Any samples with <10% missing data from any experiment were excluded from any further analysis.
Prior to association anlysis, all cluster plots were visually and/or manually checked to check that the SNP had been genotyped well and to confirm that the calling algorithm had correctly called the clusters.
Other criteria applied to the data included call rate >95% in case or control and HW P>10-4 in each control sample.
GDXHsS00011 meets the following criteria: