Cell Specific eQTL Analysis without Sorting Cells

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-envir...

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Main Authors:	Westra, Harm-Jan, Arends, Danny, Esko, Tõnu, Peters, Marjolein J., Schurmann, Claudia, Schramm, Katharina, Kettunen, Johannes, Yaghootkar, Hanieh, Fairfax, Benjamin P., Andiappan, Anand Kumar, Li, Yang, Fu, Jingyuan, Karjalainen, Juha, Platteel, Mathieu, Visschedijk, Marijn, Weersma, Rinse K., Kasela, Silva, Milani, Lili, Tserel, Liina, Peterson, Pärt, Reinmaa, Eva, Hofman, Albert, Uitterlinden, André G., Rivadeneira, Fernando, Homuth, Georg, Petersmann, Astrid, Lorbeer, Roberto, Prokisch, Holger, Meitinger, Thomas, Herder, Christian, Roden, Michael, Grallert, Harald, Ripatti, Samuli, Perola, Markus, Wood, Andrew R., Melzer, David, Ferrucci, Luigi, Singleton, Andrew B., Hernandez, Dena G., Knight, Julian C., Melchiotti, Rossella, Lee, Bernett, Poidinger, Michael, Zolezzi, Francesca, Larbi, Anis, Wang, De Yun, van den Berg, Leonard H., Veldink, Jan H., Rotzschke, Olaf, Makino, Seiko, Salomaa, Veikko, Strauch, Konstantin, Völker, Uwe, van Meurs, Joyce B. J., Metspalu, Andres, Wijmenga, Cisca, Jansen, Ritsert C., Franke, Lude
Format:	Online
Language:	English
Published:	Public Library of Science 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4425538/

id	pubmed-4425538
recordtype	oai_dc
spelling	pubmed-44255382015-05-21 Cell Specific eQTL Analysis without Sorting Cells Westra, Harm-Jan Arends, Danny Esko, Tõnu Peters, Marjolein J. Schurmann, Claudia Schramm, Katharina Kettunen, Johannes Yaghootkar, Hanieh Fairfax, Benjamin P. Andiappan, Anand Kumar Li, Yang Fu, Jingyuan Karjalainen, Juha Platteel, Mathieu Visschedijk, Marijn Weersma, Rinse K. Kasela, Silva Milani, Lili Tserel, Liina Peterson, Pärt Reinmaa, Eva Hofman, Albert Uitterlinden, André G. Rivadeneira, Fernando Homuth, Georg Petersmann, Astrid Lorbeer, Roberto Prokisch, Holger Meitinger, Thomas Herder, Christian Roden, Michael Grallert, Harald Ripatti, Samuli Perola, Markus Wood, Andrew R. Melzer, David Ferrucci, Luigi Singleton, Andrew B. Hernandez, Dena G. Knight, Julian C. Melchiotti, Rossella Lee, Bernett Poidinger, Michael Zolezzi, Francesca Larbi, Anis Wang, De Yun van den Berg, Leonard H. Veldink, Jan H. Rotzschke, Olaf Makino, Seiko Salomaa, Veikko Strauch, Konstantin Völker, Uwe van Meurs, Joyce B. J. Metspalu, Andres Wijmenga, Cisca Jansen, Ritsert C. Franke, Lude Research Article 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. Public Library of Science 2015-05-08 /pmc/articles/PMC4425538/ /pubmed/25955312 http://dx.doi.org/10.1371/journal.pgen.1005223 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Westra, Harm-Jan Arends, Danny Esko, Tõnu Peters, Marjolein J. Schurmann, Claudia Schramm, Katharina Kettunen, Johannes Yaghootkar, Hanieh Fairfax, Benjamin P. Andiappan, Anand Kumar Li, Yang Fu, Jingyuan Karjalainen, Juha Platteel, Mathieu Visschedijk, Marijn Weersma, Rinse K. Kasela, Silva Milani, Lili Tserel, Liina Peterson, Pärt Reinmaa, Eva Hofman, Albert Uitterlinden, André G. Rivadeneira, Fernando Homuth, Georg Petersmann, Astrid Lorbeer, Roberto Prokisch, Holger Meitinger, Thomas Herder, Christian Roden, Michael Grallert, Harald Ripatti, Samuli Perola, Markus Wood, Andrew R. Melzer, David Ferrucci, Luigi Singleton, Andrew B. Hernandez, Dena G. Knight, Julian C. Melchiotti, Rossella Lee, Bernett Poidinger, Michael Zolezzi, Francesca Larbi, Anis Wang, De Yun van den Berg, Leonard H. Veldink, Jan H. Rotzschke, Olaf Makino, Seiko Salomaa, Veikko Strauch, Konstantin Völker, Uwe van Meurs, Joyce B. J. Metspalu, Andres Wijmenga, Cisca Jansen, Ritsert C. Franke, Lude
spellingShingle	Westra, Harm-Jan Arends, Danny Esko, Tõnu Peters, Marjolein J. Schurmann, Claudia Schramm, Katharina Kettunen, Johannes Yaghootkar, Hanieh Fairfax, Benjamin P. Andiappan, Anand Kumar Li, Yang Fu, Jingyuan Karjalainen, Juha Platteel, Mathieu Visschedijk, Marijn Weersma, Rinse K. Kasela, Silva Milani, Lili Tserel, Liina Peterson, Pärt Reinmaa, Eva Hofman, Albert Uitterlinden, André G. Rivadeneira, Fernando Homuth, Georg Petersmann, Astrid Lorbeer, Roberto Prokisch, Holger Meitinger, Thomas Herder, Christian Roden, Michael Grallert, Harald Ripatti, Samuli Perola, Markus Wood, Andrew R. Melzer, David Ferrucci, Luigi Singleton, Andrew B. Hernandez, Dena G. Knight, Julian C. Melchiotti, Rossella Lee, Bernett Poidinger, Michael Zolezzi, Francesca Larbi, Anis Wang, De Yun van den Berg, Leonard H. Veldink, Jan H. Rotzschke, Olaf Makino, Seiko Salomaa, Veikko Strauch, Konstantin Völker, Uwe van Meurs, Joyce B. J. Metspalu, Andres Wijmenga, Cisca Jansen, Ritsert C. Franke, Lude Cell Specific eQTL Analysis without Sorting Cells
author_facet	Westra, Harm-Jan Arends, Danny Esko, Tõnu Peters, Marjolein J. Schurmann, Claudia Schramm, Katharina Kettunen, Johannes Yaghootkar, Hanieh Fairfax, Benjamin P. Andiappan, Anand Kumar Li, Yang Fu, Jingyuan Karjalainen, Juha Platteel, Mathieu Visschedijk, Marijn Weersma, Rinse K. Kasela, Silva Milani, Lili Tserel, Liina Peterson, Pärt Reinmaa, Eva Hofman, Albert Uitterlinden, André G. Rivadeneira, Fernando Homuth, Georg Petersmann, Astrid Lorbeer, Roberto Prokisch, Holger Meitinger, Thomas Herder, Christian Roden, Michael Grallert, Harald Ripatti, Samuli Perola, Markus Wood, Andrew R. Melzer, David Ferrucci, Luigi Singleton, Andrew B. Hernandez, Dena G. Knight, Julian C. Melchiotti, Rossella Lee, Bernett Poidinger, Michael Zolezzi, Francesca Larbi, Anis Wang, De Yun van den Berg, Leonard H. Veldink, Jan H. Rotzschke, Olaf Makino, Seiko Salomaa, Veikko Strauch, Konstantin Völker, Uwe van Meurs, Joyce B. J. Metspalu, Andres Wijmenga, Cisca Jansen, Ritsert C. Franke, Lude
author_sort	Westra, Harm-Jan
title	Cell Specific eQTL Analysis without Sorting Cells
title_short	Cell Specific eQTL Analysis without Sorting Cells
title_full	Cell Specific eQTL Analysis without Sorting Cells
title_fullStr	Cell Specific eQTL Analysis without Sorting Cells
title_full_unstemmed	Cell Specific eQTL Analysis without Sorting Cells
title_sort	cell specific eqtl analysis without sorting cells
description	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.
publisher	Public Library of Science
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4425538/
_version_	1613221324900007936

Cell Specific eQTL Analysis without Sorting Cells

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