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Expression Quantitative Trait Loci (eQTL) Mapping in Korean Patients With Crohn's Disease and Identification of Potential Causal Genes Through Integration With Disease Associations

Cited 12 time in Web of Science Cited 13 time in Scopus
Authors

Jung, Seulgi; Liu, Wenting; Baek, Jiwon; Moon, Jung Won; Ye, Byong Duk; Lee, Ho-Su; Park, Sang Hyoung; Yang, Suk-Kyun; Han, Buhm; Liu, Jianjun; Song, Kyuyoung

Issue Date
2020-05
Publisher
Frontiers Media S.A.
Citation
Frontiers in Genetics, Vol.11, p. 486
Abstract
Background Expression quantitative trait loci (eQTL) datasets have extensively been used to help interpret genome-wide association study signals. Most eQTL analyses have been conducted with populations of European ancestry. Objective To determine the most functionally relevant genes at the Crohn's disease (CD) loci identified in genome-wide association studies (GWAS) involving Asian populations and to find novel disease-associated genes, we conducted an eQTL analysis. Methods eQTL analysis was performed using whole-blood RNA-sequencing of 101 Korean patients with CD. FastQTL was used for a pair-wise genome analysis of similar to 6.5 M SNPs and similar to 22 K transcripts. Results We identified 135,164 cis-eQTL and 3,816 eGenes with a false discovery rate less than 0.05. A significant proportion of the genes identified in our study overlapped with those identified in previous studies. The significantly enriched pathways of these 3,816 eGenes included neutrophil degranulation and small molecule biosynthetic process. Integrated analysis of CD GWAS with Korean eQTL revealed two putative target genes, TNFSF15 and GPR35, at two previously reported loci, whereas TNFSF15 only with the whole blood data from the Genotype-Tissue Expression (GTEx) project, highlighting the utility of building a population-specific data set, even of modest size. The risk alleles of these genes were found to be associated with lower expression levels of TNFSF15 and GPR35, respectively. Our eQTL browser can be accessed at "". Conclusion This resource would be useful for studies that need to employ genome-wide association analyses involving Asian populations.
ISSN
1664-8021
URI
https://hdl.handle.net/10371/191488
DOI
https://doi.org/10.3389/fgene.2020.00486
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