Cell Specific eQTL Analysis without Sorting Cells.

PLoS Genetics. 2015;11(5):e1005223 DOI 10.1371/journal.pgen.1005223

 

Journal Homepage

Journal Title: PLoS Genetics

ISSN: 1553-7390 (Print); 1553-7404 (Online)

Publisher: Public Library of Science (PLoS)

LCC Subject Category: Science: Biology (General): Genetics

Country of publisher: United States

Language of fulltext: English

Full-text formats available: PDF, HTML, XML

 

AUTHORS


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

EDITORIAL INFORMATION

Peer review

Editorial Board

Instructions for authors

Time From Submission to Publication: 26 weeks

 

Abstract | Full Text

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.