Genes in Inflammatory Bowel Disease-Associated Risk Loci Demonstrate Genotype-, Tissue-, and Inflammation-Specific Patterns of Expression in Terminal Ileum and Colon Mucosal Tissue

With a greater understanding of the genetic risk variants associated with inflammatory bowel disease, there is a need to prioritize candidate genes within risk loci leading to the disease-SNP association. We created a custom NanoString probeset to capture 678 genes of interest in IBD (including 440 genes encoded within IBD risk loci and 15 housekeeping genes) - 22% of genes were not captured on traditional microarray platforms. Total RNA extracted from terminal ileum and colon tissues (uninflamed and inflamed) was used from patients with Crohn's disease and ulcerative colitis and healthy controls. We studied differential expression and performed an eQTL analysis to prioritize candidate genes within the risk loci. Gene expression profiles were generated for uninflamed and inflamed, colon and TI tissues from patients with inflammatory bowel disease and healthy controls on the NanoString platform.