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Title: Cell Specific eQTL Analysis without Sorting Cells
Authors: Westra H.-J.
Arends D.
Esko T.
Peters M.J.
Schurmann C.
Schramm K.
Kettunen J.
Yaghootkar H.
Fairfax B.P.
Andiappan A.K.
Li Y.
Fu J.
Karjalainen J.
Platteel M.
Visschedijk M.
Weersma R.K.
Kasela S.
Milani L.
Tserel L.
Peterson P.
Reinmaa E.
Hofman A.
Uitterlinden A.G.
Rivadeneira F.
Homuth G.
Petersmann A.
Lorbeer R.
Prokisch H.
Meitinger T.
Herder C.
Roden M.
Grallert H.
Ripatti S.
Perola M.
Wood A.R.
Melzer D.
Ferrucci L.
Singleton A.B.
Hernandez D.G.
Knight J.C.
Melchiotti R.
Lee B.
Poidinger M. 
Zolezzi F.
Larbi A. 
Wang D.Y. 
van den Berg L.H.
Veldink J.H.
Rotzschke O.
Makino S.
Salomaa V.
Strauch K.
Völker U.
van Meurs J.B.J.
Metspalu A.
Wijmenga C.
Jansen R.C.
Franke L.
Keywords: caspase recruitment domain protein 15
caspase recruitment domain protein 15
NOD2 protein, human
cell selection
cell specificity
cohort analysis
controlled study
Crohn disease
downstream processing
gene expression profiling
genotype environment interaction
NOD2 gene
quantitative trait locus mapping
single nucleotide polymorphism
cell line
gene expression regulation
genome-wide association study
meta analysis
principal component analysis
quantitative trait locus
single nucleotide polymorphism
Cell Line
Crohn Disease
Gene Expression Regulation
Genome-Wide Association Study
Nod2 Signaling Adaptor Protein
Polymorphism, Single Nucleotide
Principal Component Analysis
Quantitative Trait Loci
Reproducibility of Results
Issue Date: 2015
Publisher: Public Library of Science
Citation: Westra H.-J., Arends D., Esko T., Peters M.J., Schurmann C., Schramm K., Kettunen J., Yaghootkar H., Fairfax B.P., Andiappan A.K., Li Y., Fu J., Karjalainen J., Platteel M., Visschedijk M., Weersma R.K., Kasela S., Milani L., Tserel L., Peterson P., Reinmaa E., Hofman A., Uitterlinden A.G., Rivadeneira F., Homuth G., Petersmann A., Lorbeer R., Prokisch H., Meitinger T., Herder C., Roden M., Grallert H., Ripatti S., Perola M., Wood A.R., Melzer D., Ferrucci L., Singleton A.B., Hernandez D.G., Knight J.C., Melchiotti R., Lee B., Poidinger M., Zolezzi F., Larbi A., Wang D.Y., van den Berg L.H., Veldink J.H., Rotzschke O., Makino S., Salomaa V., Strauch K., Völker U., van Meurs J.B.J., Metspalu A., Wijmenga C., Jansen R.C., Franke L. (2015). Cell Specific eQTL Analysis without Sorting Cells. PLoS Genetics 11 (5) : e1005223. ScholarBank@NUS Repository.
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. © 2015, Public Library of Science. All rights reserved.
Source Title: PLoS Genetics
ISSN: 15537390
DOI: 10.1371/journal.pgen.1005223
Appears in Collections:Staff Publications

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