Meta-analysis of six ulcerative colitis (UC) disease genome wide association studies (GWAS) comprising 6,687 affected individuals (cases) and 19,718 controls of European descent. Genotyping in the six studies was performed on Illumina Hap370 or 610-Quad platforms. Imputation was carried out using the IMPUTE software. In total, 50 SNPs were selected for follow-up in 9,628 cases and 12,917 controls. This identified 29 new risk loci, bringing the total of ulcerative colitis associated loci to 47 (note - 2 previously identified loci do not meet genome-wide significance in this study).
Any individuls or samples with <10% missing data were removed.
Duplicate samples across cohorts were identified and the sample with the lowest call rate was removed.
Hardy-Weinberg equilibrium (HWE) P<10-4
For eQTL Analysis, SNPs were excluded as below:-
- Minor allele frequency < 5%
- Call rate < 95%
- Hardy-Weinbery equilibrium (HWE) P<10-3
GDXHsS00029 meets the following criteria: