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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.
  • Westra HJ; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
  • Arends D; Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands.
  • Esko T; Estonian Genome Center, University of Tartu, Tartu, Estonia; Divisions of Endocrinology, Boston Children's Hospital, Boston, Massachusetts, United States of America; Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America; Broad Institute, Cambridge, Massachus
  • Peters MJ; Department of Internal Medicine, Erasmus Medical Centre Rotterdam, the Netherlands; The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/ Rotterdam, the Netherlands.
  • Schurmann C; Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany; The Charles Bronfman Institute for Personalized Medicine, Genetics of Obesity & Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, New York, United S
  • Schramm K; Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institut für Humangenetik, Technische Universität München, München, Germany.
  • Kettunen J; Computational Medicine, Institute of Health Sciences, Faculty of Medicine, University of Oulu, Oulu, Finland; Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland; Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finla
  • Yaghootkar H; Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom.
  • Fairfax BP; Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom; Department of Oncology, Cancer and Haematology Centre, Churchill Hospital, Oxford, United Kingdom.
  • Andiappan AK; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore.
  • Li Y; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands.
  • Fu J; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
  • Karjalainen J; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
  • Platteel M; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
  • Visschedijk M; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.
  • Weersma RK; University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.
  • Kasela S; Estonian Genome Center, University of Tartu, Tartu, Estonia; Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
  • Milani L; Estonian Genome Center, University of Tartu, Tartu, Estonia.
  • Tserel L; Molecular Pathology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.
  • Peterson P; Molecular Pathology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.
  • Reinmaa E; Estonian Genome Center, University of Tartu, Tartu, Estonia.
  • Hofman A; The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/ Rotterdam, the Netherlands; Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands.
  • Uitterlinden AG; Department of Internal Medicine, Erasmus Medical Centre Rotterdam, the Netherlands; The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/ Rotterdam, the Netherlands; Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, the Neth
  • Rivadeneira F; Department of Internal Medicine, Erasmus Medical Centre Rotterdam, the Netherlands; The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/ Rotterdam, the Netherlands; Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, the Neth
  • Homuth G; Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
  • Petersmann A; Institute for Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany.
  • Lorbeer R; Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.
  • Prokisch H; Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institut für Humangenetik, Technische Universität München, München, Germany.
  • Meitinger T; Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institut für Humangenetik, Technische Universität München, München, Germany; Munich Heart Alliance, Munich, Germany; German Center for Cardiovascular Research (DZHK), Germany
  • Herder C; Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany; German Center for Diabetes Research (DZD), partner site Düsseldorf, Düsseldorf, Germany.
  • Roden M; Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany; German Center for Diabetes Research (DZD), partner site Düsseldorf, Düsseldorf, Germany; Department of Diabetology and Endocrinology, Univers
  • Grallert H; Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
  • Ripatti S; Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland; Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland; Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom; Department of Public Health, Hjelt In
  • Perola M; Estonian Genome Center, University of Tartu, Tartu, Estonia; Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland.
  • Wood AR; Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom.
  • Melzer D; Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, United Kingdom.
  • Ferrucci L; Clinical Research Branch, National Institute on Aging NIA-ASTRA Unit, Harbor Hospital, Baltimore, Maryland, United States of America.
  • Singleton AB; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America.
  • Hernandez DG; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America; Department of Molecular Neuroscience and Reta Lila Laboratories, Institute of Neurology, UCL, London, United Kingdom.
  • Knight JC; Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.
  • Melchiotti R; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore; Doctoral School in Translational and Molecular Medicine (DIMET), University of Milano-Bicocca, Milan, Italy.
  • Lee B; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore.
  • Poidinger M; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore.
  • Zolezzi F; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore.
  • Larbi A; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore.
  • Wang de Y; Department of Otolaryngology, National University of Singapore, Singapore.
  • van den Berg LH; Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, The Netherlands.
  • Veldink JH; Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, The Netherlands.
  • Rotzschke O; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore.
  • Makino S; Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.
PLoS Genet ; 11(5): e1005223, 2015 May.
Article en En | MEDLINE | ID: mdl-25955312
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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Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Linfocitos / Polimorfismo de Nucleótido Simple / Sitios de Carácter Cuantitativo / Neutrófilos Tipo de estudio: Prognostic_studies / Systematic_reviews Límite: Humans Idioma: En Año: 2015 Tipo del documento: Article
Texto completo
Imprimir
XML
PubMed Links
Search on Google

Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Linfocitos / Polimorfismo de Nucleótido Simple / Sitios de Carácter Cuantitativo / Neutrófilos Tipo de estudio: Prognostic_studies / Systematic_reviews Límite: Humans Idioma: En Año: 2015 Tipo del documento: Article