PLoS Genetics (May 2015)
Cell Specific eQTL Analysis without Sorting Cells.
- Harm-Jan Westra,
- Danny Arends,
- Tõnu Esko,
- Marjolein J Peters,
- Claudia Schurmann,
- Katharina Schramm,
- Johannes Kettunen,
- Hanieh Yaghootkar,
- Benjamin P Fairfax,
- Anand Kumar Andiappan,
- Yang Li,
- Jingyuan Fu,
- Juha Karjalainen,
- Mathieu Platteel,
- Marijn Visschedijk,
- Rinse K Weersma,
- Silva Kasela,
- Lili Milani,
- Liina Tserel,
- Pärt Peterson,
- Eva Reinmaa,
- Albert Hofman,
- André G Uitterlinden,
- Fernando Rivadeneira,
- Georg Homuth,
- Astrid Petersmann,
- Roberto Lorbeer,
- Holger Prokisch,
- Thomas Meitinger,
- Christian Herder,
- Michael Roden,
- Harald Grallert,
- Samuli Ripatti,
- Markus Perola,
- Andrew R Wood,
- David Melzer,
- Luigi Ferrucci,
- Andrew B Singleton,
- Dena G Hernandez,
- Julian C Knight,
- Rossella Melchiotti,
- Bernett Lee,
- Michael Poidinger,
- Francesca Zolezzi,
- Anis Larbi,
- De Yun Wang,
- Leonard H van den Berg,
- Jan H Veldink,
- Olaf Rotzschke,
- Seiko Makino,
- Veikko Salomaa,
- Konstantin Strauch,
- Uwe Völker,
- Joyce B J van Meurs,
- Andres Metspalu,
- Cisca Wijmenga,
- Ritsert C Jansen,
- Lude Franke
Affiliations
- Harm-Jan Westra
- Danny Arends
- Tõnu Esko
- Marjolein J Peters
- Claudia Schurmann
- Katharina Schramm
- Johannes Kettunen
- Hanieh Yaghootkar
- Benjamin P Fairfax
- Anand Kumar Andiappan
- Yang Li
- Jingyuan Fu
- Juha Karjalainen
- Mathieu Platteel
- Marijn Visschedijk
- Rinse K Weersma
- Silva Kasela
- Lili Milani
- Liina Tserel
- Pärt Peterson
- Eva Reinmaa
- Albert Hofman
- André G Uitterlinden
- Fernando Rivadeneira
- Georg Homuth
- Astrid Petersmann
- Roberto Lorbeer
- Holger Prokisch
- Thomas Meitinger
- Christian Herder
- Michael Roden
- Harald Grallert
- Samuli Ripatti
- Markus Perola
- Andrew R Wood
- David Melzer
- Luigi Ferrucci
- Andrew B Singleton
- Dena G Hernandez
- Julian C Knight
- Rossella Melchiotti
- Bernett Lee
- Michael Poidinger
- Francesca Zolezzi
- Anis Larbi
- De Yun Wang
- Leonard H van den Berg
- Jan H Veldink
- Olaf Rotzschke
- Seiko Makino
- Veikko Salomaa
- Konstantin Strauch
- Uwe Völker
- Joyce B J van Meurs
- Andres Metspalu
- Cisca Wijmenga
- Ritsert C Jansen
- Lude Franke
- DOI
- https://doi.org/10.1371/journal.pgen.1005223
- Journal volume & issue
-
Vol. 11,
no. 5
p. e1005223
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.
