Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs

BMC Genomics
Xiaoling ZhangAndrew D Johnson

Abstract

Gene expression genetic studies in human tissues and cells identify cis- and trans-acting expression quantitative trait loci (eQTLs). These eQTLs provide insights into regulatory mechanisms underlying disease risk. However, few studies systematically characterized eQTL results across cell and tissues types. We synthesized eQTL results from >50 datasets, including new primary data from human brain, peripheral plaque and kidney samples, in order to discover features of human eQTLs. We find a substantial number of robust cis-eQTLs and far fewer trans-eQTLs consistent across tissues. Analysis of 45 full human GWAS scans indicates eQTLs are enriched overall, and above nSNPs, among positive statistical signals in genetic mapping studies, and account for a significant fraction of the strongest human trait effects. Expression QTLs are enriched for gene centricity, higher population allele frequencies, in housekeeping genes, and for coincidence with regulatory features, though there is little evidence of 5' or 3' positional bias. Several regulatory categories are not enriched including microRNAs and their predicted binding sites and long, intergenic non-coding RNAs. Among the most tissue-ubiquitous cis-eQTLs, there is enrichment for gen...Continue Reading

Citations

Mar 21, 2015·Nature Communications·Tianxiao HuanJane E Freedman
Nov 28, 2014·Nucleic Acids Research·John D EicherAndrew D Johnson
Jun 28, 2016·American Journal of Human Genetics·Nathalie ChamiGuillaume Lettre
Jun 28, 2016·American Journal of Human Genetics·John D EicherAndrew D Johnson
May 23, 2017·Nature Genetics·Joanna M M HowsonDanish Saleheen
Jun 21, 2017·Genome Biology·Catherine DoBenjamin Tycko
Jul 13, 2019·European Journal of Human Genetics : EJHG·Akira Mizuno, Yukinori Okada
Oct 23, 2019·Nature Genetics·Claudia L SatizabalM Arfan Ikram
Mar 2, 2019·Nature Genetics·Brian W KunkleGenetic and Environmental Risk in AD/Defining Genetic, Polygenic and Environmental Risk for Alzheimer’s Disease Consortium (
Jun 6, 2017·Experimental Biology and Medicine·Yizhou ZhuYousin Suh
Apr 28, 2017·PLoS Genetics·Mariaelisa GraffTuomas O Kilpeläinen

Datasets Mentioned

BETA
GM12878

Methods Mentioned

BETA
footprinting
ChIP-seq
genotyping

Related Concepts

Genetic Equilibrium
Tissue Specificity
Disease Clustering
Single Nucleotide Polymorphism
MRNA Differential Display
Quantitative Trait Loci
Genome-Wide Association Study
Gene Expression Profiles
Alleles
Brain

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