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Analysis Name and Accession
Name: A Genome-Wide Association Study on Inflammatory Bowel Disease
Accession: pha002847.1

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Analysis Description
This dataset contains data from a genome-wide association study performed with 968 IBD-affected cases and 995 unrelated controls using the Illumina HumanHap300 Genotyping BeadChip. Cases were selected to have Crohn's disease with ileal involvement, and controls were matched to cases based on sex and year of birth. Subjects were drawn from two cohorts: (1) persons with non-Jewish, European ancestry (561 cases and 563 controls), and (2) persons with Jewish ancestry (407 cases and 432 controls). Genotyping was performed at the Feinstein Institute for Medical Research.
Analysis Methods
SNPs were excluded for call rates less than 95% and/or MAF less than 1%. In addition, of the 1,963 original samples, 51 were excluded because they had overall call rates less than 93%. This left 395 cases and 431 controls in the Jewish stratum, and 544 cases and 542 controls in the non-Jewish stratum. We then performed a stratified analysis to test case/control association among both the Jewish and non-Jewish cohorts, using a Cochran-Mantel Haenszel chi-square test computed separately for each SNP as implemented in PLINK v1.01. Asymptotic p-values are reported.
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