Enrichment of inflammatory bowel disease and colorectal cancer risk variants in colon expression quantitative trait loci

BMC Genomics
Imge HulurSonia S Kupfer

Abstract

Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with diseases of the colon including inflammatory bowel diseases (IBD) and colorectal cancer (CRC). However, the functional role of many of these SNPs is largely unknown and tissue-specific resources are lacking. Expression quantitative trait loci (eQTL) mapping identifies target genes of disease-associated SNPs. This study provides a comprehensive eQTL map of distal colonic samples obtained from 40 healthy African Americans and demonstrates their relevance for GWAS of colonic diseases. 8.4 million imputed SNPs were tested for their associations with 16,252 expression probes representing 12,363 unique genes. 1,941 significant cis-eQTL, corresponding to 122 independent signals, were identified at a false discovery rate (FDR) of 0.01. Overall, among colon cis-eQTL, there was significant enrichment for GWAS variants for IBD (Crohn's disease [CD] and ulcerative colitis [UC]) and CRC as well as type 2 diabetes and body mass index. ERAP2, ADCY3, INPP5E, UBA7, SFMBT1, NXPE1 and REXO2 were identified as target genes for IBD-associated variants. The CRC-associated eQTL rs3802842 was associated with the expression of C11orf93 (COLCA2)...Continue Reading

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Jun 24, 2016·Clinical and Translational Gastroenterology·Antonio F Di NarzoKe Hao
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Datasets Mentioned

BETA
GSE
56789

Methods Mentioned

BETA
genotyping
biopsies
PCA

Software Mentioned

EIGENSTRAT
Illumina GenomeStudio
BLAST
Matrix eQTL R package
GTEx eQTL browser
IMPUTE2
Bioconductor
Illumina Genome Studio
R

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