Identification of context-dependent expression quantitative trait loci in whole blood
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Publication date
2017-01
Authors
Zhernakova, Daria V
Deelen, Patrick
Vermaat, Martijn
van Iterson, Maarten
van Galen, Michiel
Arindrarto, Wibowo
van 't Hof, Peter
Mei, Hailiang
van Dijk, Freerk
Westra, Harm-Jan
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Document Type
Article
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taverne
Abstract
Genetic risk factors often localize to noncoding regions of the genome with unknown effects on disease etiology. Expression quantitative trait loci (eQTLs) help to explain the regulatory mechanisms underlying these genetic associations. Knowledge of the context that determines the nature and strength of eQTLs may help identify cell types relevant to pathophysiology and the regulatory networks underlying disease. Here we generated peripheral blood RNA-seq data from 2,116 unrelated individuals and systematically identified context-dependent eQTLs using a hypothesis-free strategy that does not require previous knowledge of the identity of the modifiers. Of the 23,060 significant cis-regulated genes (false discovery rate (FDR) ≤ 0.05), 2,743 (12%) showed context-dependent eQTL effects. The majority of these effects were influenced by cell type composition. A set of 145 cis-eQTLs depended on type I interferon signaling. Others were modulated by specific transcription factors binding to the eQTL SNPs.
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Taverne, Journal Article
Citation
Zhernakova, D V, Deelen, P, Vermaat, M, van Iterson, M, van Galen, M, Arindrarto, W, van 't Hof, P, Mei, H, van Dijk, F, Westra, H-J, Bonder, M J, van Rooij, J, Verkerk, M, Jhamai, P M, Moed, M, Kielbasa, S M, Bot, J, Nooren, I, Pool, R, van Dongen, J, Hottenga, J J, Stehouwer, C D A, van der Kallen, C J H, Schalkwijk, C G, Zhernakova, A, Li, Y, Tigchelaar, E F, de Klein, N, Beekman, M, Deelen, J, van Heemst, D, van den Berg, L H, Hofman, A, Uitterlinden, A G, van Greevenbroek, M M J, Veldink, J H, Boomsma, D I, van Duijn, C M, Wijmenga, C, Slagboom, P E, Swertz, M A, Isaacs, A, van Meurs, J B J, Jansen, R, Heijmans, B T, 't Hoen, P A C & Franke, L 2017, 'Identification of context-dependent expression quantitative trait loci in whole blood', Nature Genetics, vol. 49, no. 1, pp. 139–145. https://doi.org/10.1038/ng.3737