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eQTL mapping identifies insertion- and deletion-specific eQTLs in multiple tissues

Official URL:https://doi.org/10.1038/ncomms7821
PubMed:View item in PubMed
Creators Name:Huang, J. and Chen, J. and Esparza, J. and Ding, J. and Elder, J.T. and Abecasis, G.R. and Lee, Y.A. and Lathrop, G.M. and Moffatt, M.F. and Cookson, W.O.C. and Liang, L.
Journal Title:Nature Communications
Journal Abbreviation:Nat Commun
Volume:6
Page Range:6821
Date:8 May 2015
Keywords:Chromosome Mapping, Genetic Association Studies, Genetic Epigenesis, Genome-Wide Association Study, INDEL Mutation, Meta-Analysis as Topic, Organ Specificity, Quantitative Trait Loci, Single Nucleotide Polymorphism
Abstract:Genome-wide gene expression quantitative trait loci (eQTL) mapping have been focused on single-nucleotide polymorphisms and have helped interpret findings from diseases mapping studies. The functional effect of structure variants, especially short insertions and deletions (indel) has not been well investigated. Here we impute 1,380,133 indels based on the latest 1,000 Genomes Project panel into three eQTL data sets from multiple tissues. Imputation of indels increased 9.9% power and identifies indel-specific eQTLs for 325 genes. We find introns and vicinities of UTRs are more enriched of indel eQTLs and 3.6 (single-tissue)-9.2%(multi-tissue) of previous identified eSNPs were taggers of eindels. Functional analyses identifies epigenetics marks, gene ontology categories and disease GWAS loci affected by SNPs and indels eQTLs showing tissue-consistent or tissue-specific effects. This study provides new insights into the underlying genetic architecture of gene expression across tissues and new resource to interpret function of diseases and traits associated structure variants.
ISSN:2041-1723
Publisher:Nature Publishing Group (U.K.)
Item Type:Article

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