Nat Genet. 2015 September ; 47(9): 979–986. doi:10.1038/ng.3359
Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

"Following quality-control (QC) and 1000 genomes imputation (Phase I - March2012), 5,956 Crohn’s disease cases, 6,968 ulcerative colitis cases and 21,770 population controls of European descent were used to perform genome-wide association studies of Crohn's disease, ulcerative colitis or IBD (Crohn's disease and ulcerative colitis) (Online Methods). Replication was undertaken using an additional 16,619 Crohn's disease cases, 13,449 ulcerative colitis cases and 31,766 population controls genotyped on the Immunochip. The replication cohort included 2,025 Crohn's disease cases, 2,770 ulcerative colitis cases and 5,051 population controls of non-European ancestry (Table 1, Supplementary Figure 1 and 2), so principal component analysis was used to assign individuals to one of four ancestral groups (European, Iranian, Indian or East Asian) (Supplementary Figure 3). Case-control association tests were performed within each ancestry group using a linear mixed model (MMM)9 (Online Methods). A fixed-effect meta-analysis was undertaken to combine summary statistics from our European-only GWAS meta-analysis with those from the European replication cohort. We next performed a Bayesian trans-ethnic meta-analysis, as implemented in Mantra, to enable heterogeneity in effect size to be correlated with genetic distance between populations, as estimated by the mean Fst across all SNPs10 (Online Methods). For the trans-ethnic meta-analysis, the 6,392 cases and 7,262 population controls of European ancestry that were present in both the GWAS and replication cohorts were excluded from the Immunochip replication study (Supplementary Figure 2). To maximise power for our solely Immunochip-based comparisons across ancestral groups, the mixed model association analysis was repeated after reinstating these individuals to the Immunochip cohort."

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