Cell Specific eQTL Analysis without Sorting Cells

HJ Westra, D Arends, T Esko, Marjolein Peters, C Schurmann, K Schramm, J Kettunen, H Yaghootkar, BP Fairfax, AK Andiappan, Y Li, JY Fu, J Karjalainen, M Platteel, M Visschedijk, RK Weersma, S Kasela, L Milani, L Tserel, P PetersonE Reinmaa, Bert Hofman, André Uitterlinden, Fernando Rivadeneira, G Homuth, A Petersmann, R Lorbeer, H Prokisch, T Meitinger, Cindy Herder, M Roden, H Grallert, S Ripatti, M Perola, AR Wood, D Melzer, L Ferrucci, AB Singleton, DG Hernandez, JC Knight, R Melchiotti, B Lee, M Poidinger, F Zolezzi, A Larbi, DY Wang, LH van den Berg, JH Veldink, O Rotzschke, S Makino, V Salomaa, K Strauch, U Volker, Joyce van Meurs, A Metspalu, C Wijmenga, RC Jansen, L Franke

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Abstract

The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL) mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-environment interaction (GxE) meta-analysis on data from 5,683 samples to infer the cell type specificity of whole blood cis-eQTLs. We demonstrate that this method is able to predict neutrophil and lymphocyte specific cis-eQTLs and replicate these predictions in independent cell-type specific datasets. Finally, we show that SNPs associated with Crohn's disease preferentially affect gene expression within neutrophils, including the archetypal NOD2 locus.
Original languageUndefined/Unknown
JournalPLoS Genetics (print)
Volume11
Issue number5
DOIs
Publication statusPublished - 2015

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