New Results
Cell specific eQTL analysis without sorting cells
View ORCID ProfileHarm-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 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, Timouthy M. Frayling, Veikko Salomaa, Konstantin Strauch, Uwe Völker, Joyce B. J. van Meurs, Andres Metspalu, Cisca Wijmenga, Ritsert C. Jansen, Lude Franke
doi: https://doi.org/10.1101/002600
Harm-Jan Westra
1University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9700RB, Groningen, The Netherlands.
Danny Arends
2Groningen Bioinformatics Centre, University of Groningen, P.O. Box 11103, 9700 CC Groningen, The Netherlands.
Tõnu Esko
3Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia.
4Divisions of Endocrinology, Boston Children's Hospital, Boston, 02115, USA.
5Department of Genetics, Harvard Medical School, Boston, 02115, USA.
6Broad Institute, Cambridge, 02142, USA.
Marjolein J. Peters
7Department of Internal Medicine, Erasmus Medical Centre Rotterdam, the Netherlands.
8The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, the Netherlands.
Claudia Schurmann
9Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15A, 17475 Greifswald, Germany.
10The Charles Bronfman Institute for Personalized Medicine, Genetics of Obesity & Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA.
Katharina Schramm
11Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
12Institut für Humangenetik, Technische Universität München, Trogerstr. 32, 81675 München, Germany.
Johannes Kettunen
13Computational Medicine, Institute of Health Sciences, Faculty of Medicine, University of Oulu, Oulu, Finland.
14Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland.
15Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland.
Hanieh Yaghootkar
16Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK.
Benjamin P. Fairfax
17Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
18Department of Oncology, Cancer and Haematology Centre, Churchill Hospital, Oxford, OX3 7LJ.
Anand Kumar Andiappan
19Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore 138648.
Yang Li
1University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9700RB, Groningen, The Netherlands.
2Groningen Bioinformatics Centre, University of Groningen, P.O. Box 11103, 9700 CC Groningen, The Netherlands.
Jingyuan Fu
1University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9700RB, Groningen, The Netherlands.
Juha Karjalainen
1University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9700RB, Groningen, The Netherlands.
Mathieu Platteel
1University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9700RB, Groningen, The Netherlands.
Marijn Visschedijk
1University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9700RB, Groningen, The Netherlands.
20University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Hanzeplein 1, 9700RB, Groningen, The Netherlands.
Rinse Weersma
20University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Hanzeplein 1, 9700RB, Groningen, The Netherlands.
Silva Kasela
3Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia.
21Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia.
Lili Milani
3Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia.
Liina Tserel
22Molecular Pathology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, Biomedicum, 50411, Tartu, Estonia.
Pärt Peterson
22Molecular Pathology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, Biomedicum, 50411, Tartu, Estonia.
Eva Reinmaa
3Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia.
Albert Hofman
8The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, the Netherlands.
23Department of Epidemiology, Erasmus Medical Center Rotterdam, the Netherlands.
André G. Uitterlinden
7Department of Internal Medicine, Erasmus Medical Centre Rotterdam, the Netherlands.
8The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, the Netherlands.
23Department of Epidemiology, Erasmus Medical Center Rotterdam, the Netherlands.
Fernando Rivadeneira
7Department of Internal Medicine, Erasmus Medical Centre Rotterdam, the Netherlands.
8The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, the Netherlands.
23Department of Epidemiology, Erasmus Medical Center Rotterdam, the Netherlands.
Georg Homuth
9Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15A, 17475 Greifswald, Germany.
Astrid Petersmann
24Institute for Clinical Chemistry and Laboratory Medcine, University Medicine Greifswald, Sauerbruchstr., 17475 Greifswald, Germany.
Roberto Lorbeer
25Institute for Community Medicine, University Medicine Greifswald, Walther-Rathenau-Str. 48, 17475 Greifswald, Germany.
Holger Prokisch
26Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
27Institut für Humangenetik, Technische Universität München, Trogerstr. 32, 81675 München, Germany.
Thomas Meitinger
26Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
27Institut für Humangenetik, Technische Universität München, Trogerstr. 32, 81675 München, Germany.
28Munich Heart Allience, Munich, Germany.
29German Center for Cardiovascular Research (DZHK), Germany.
Christian Herder
30Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Auf'm Hennekamp 65, 40225 Düsseldorf, Germany.
31German Center for Diabetes Research (DZD), partner site Düsseldorf, Germany.
Michael Roden
30Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Auf'm Hennekamp 65, 40225 Düsseldorf, Germany.
31German Center for Diabetes Research (DZD), partner site Düsseldorf, Germany.
32Department of Diabetology and Endocrinology, University Hospital Düsseldorf, Heinrich Heine University, Moorenstr. 5, 40225 Düsseldorf, Germany.
Harald Grallert
33Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
Samuli Ripatti
34Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland.
35Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland.
36Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
37Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki, Finland.
Markus Perola
3Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia.
15Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland.
Andrew R. Wood
16Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK.
David Melzer
38Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK.
Luigi Ferrucci
39Clinical Research Branch, National Institute on Aging NIAASTRA Unit, Harbor Hospital, MD, USA.
Andrew B. Singleton
40Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Lincoln Drive, Bethesda, MD, USA.
Dena G. Hernandez
40Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, 35 Lincoln Drive, Bethesda, MD, USA.
41Department of Molecular Neuroscience and Reta Lila Laboratories, Institute of Neurology, UCL, Queen Square House, Queen Square, London WC1N 3BG, UK.
Julian C. Knight
17Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
Rossella Melchiotti
19Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore 138648.
42Doctoral School in Translational and Molecular Medicine (DIMET), University of Milano-Bicocca, Piazza della Scienza, 3, 20126 Milan, Italy.
Bernett Lee
19Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore 138648.
Michael Poidinger
19Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore 138648.
Francesca Zolezzi
19Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore 138648.
Anis Larbi
19Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore 138648.
De Yun Wang
43Department of Otolaryngology, National University of Singapore, Singapore.
Leonard H. van den Berg
44Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, The Netherlands.
Jan H. Veldink
44Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, The Netherlands.
Olaf Rotzschke
19Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore 138648.
Seiko Makino
17Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
Timouthy M. Frayling
16Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK.
Veikko Salomaa
15Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland.
Konstantin Strauch
45Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
46Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
Uwe Völker
9Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15A, 17475 Greifswald, Germany.
Joyce B. J. van Meurs
7Department of Internal Medicine, Erasmus Medical Centre Rotterdam, the Netherlands.
8The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, the Netherlands.
Andres Metspalu
3Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia.
Cisca Wijmenga
1University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9700RB, Groningen, The Netherlands.
Ritsert C. Jansen
2Groningen Bioinformatics Centre, University of Groningen, P.O. Box 11103, 9700 CC Groningen, The Netherlands.
Lude Franke
1University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9700RB, Groningen, The Netherlands.
Abstract
Expression quantitative trait locus (eQTL) mapping on tissue, organ or whole organism data can detect associations that are generic across cell types. We describe a new method to focus upon specific cell types without first needing to sort cells. We applied the method to whole blood data from 5,683 samples and demonstrate that SNPs associated with Crohn's disease preferentially affect gene expression within neutrophils.
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Posted February 12, 2014.
Cell specific eQTL analysis without sorting cells
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 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, Timouthy M. Frayling, Veikko Salomaa, Konstantin Strauch, Uwe Völker, Joyce B. J. van Meurs, Andres Metspalu, Cisca Wijmenga, Ritsert C. Jansen, Lude Franke
bioRxiv 002600; doi: https://doi.org/10.1101/002600
Cell specific eQTL analysis without sorting cells
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 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, Timouthy M. Frayling, Veikko Salomaa, Konstantin Strauch, Uwe Völker, Joyce B. J. van Meurs, Andres Metspalu, Cisca Wijmenga, Ritsert C. Jansen, Lude Franke
bioRxiv 002600; doi: https://doi.org/10.1101/002600
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