A GWA scan of 5,956 cases and 14,927 controls for Crohn's disease (CD) was carried out using HapMap phase 3 (CEU+TSI) data to impute 1.23M SNPs. Imputation was carried out using Beagle 3.1 and association was calculated using PLINK. A meta-analysis was perfomed by combining the above, filtered by P.association < 0.01, with a replication cohort of 14,763 Crohn's disease cases and 15,977 controls genotyped on the ImmunoChip platform. This identified 30 (16 novel) loci specific to Crohn's disease with a further 76 (24 novel) being indistinguishable from the related IBD disorder, ulcerative colitis. A further 64 loci reached genomewide significance in a combined analysis of Crohn's disease and ulcerative colitis (IBD), these are shown on the IBD study page
Group | Phenotype | Population | Cases | Controls | Families | Trios |
---|---|---|---|---|---|---|
Discovery | CRO | 5937 | 8043 | - | - | |
Replication | CRO | 14763 | 15977 | - | - |
Discovery
In addition to previously reported cohort QC, samples were excluded due to...
Markers were excluded due to...
Replication
Samples
Markers