Cell Specific eQTL Analysis without Sorting Cells

PLoS Genetics
Harm-Jan WestraLude Franke


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

laser capture micro-dissection

Related Concepts

NOD2 protein, human
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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