Overview

A trans-ancestry association study of Ulcerative Colitis and Crohns' Disease patients with genome-wide or immunochip data from 86,640 European individuals and immunochip data from 9,846 individuals of East Asian, Indian or Iranian descent.  Genotyping was performed on a combination of the Affymetrix GeneChip 500K, Affymetrix Array 6.0, Illumina Hap300 and Hap550 BeadChip arrays.  Imputation was carried out using IMPUTE2/SHAPEIT approaches against the full 1000 Genomes Project dataset.  A total of 144,245 SNPs were available for analysis in the European data set.  In total 201 loci were identified as significant in at least one of UC, CRO or IBD, of which 38 were new.

Study Type
Case-Control Study
Samples
GroupPhenotypePopulationCasesControlsFamiliesTrios
DiscoveryCROCEU595614927--
DiscoveryIBDCEU1288221770--
DiscoveryUCCEU696820464--
ReplicationCROCEU14594---
ReplicationIBDCEU-26715--
ReplicationUCCEU10679---
Exclusion Criteria

SNPs were excluded as below:-

  • Non-autosomal
  • Call rate < 98%
  • Hardy-Weinbery equilibrium (HWE) P<10-5
  • Missing from the 1000 Genomes Project Phase I data
  • Monomorphic in the population
  • Had different missing geneotype rates for cases and controls

Samples were excluded as below:-

  • Low call rate (< 98%)
  • Outlying heterozygosity rate < 0.01
  • Identity by decent with another sample > 0.8

Study Association

Criteria

GDXHsS00051 meets the following criteria:

Criteria Name
Details
Disease Tags
Study for a Disease 

Publications

PMIDTitleFirst AuthorJournalDisease(s)Date