Cell Specific eQTL Analysis without Sorting Cells

PLoS Genetics
Harm-Jan WestraLude Franke

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.

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Methods Mentioned

BETA
laser capture micro-dissection
RNA-seq
PCA
dissection
MDS

Related Concepts

NOD2 protein, human
IIeocolitis
Lymphoid Cells
Neutrophil Band Cells
Reproducibility of Results
Single Nucleotide Polymorphism
Principal Component Analysis
Quantitative Trait Loci
Nod2 Signaling Adaptor Protein
Genome-Wide Association Study

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