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Moutsianas L, Jostins L, Beecham AH, Dilthey AT, Xifara DK, Ban M, Shah TS, Patsopoulos NA, Alfredsson L, Anderson CA, Attfield KE, Baranzini SE, Barrett J, Binder TMC, Booth D, Buck D, Celius EG, Cotsapas C, D'Alfonso S, Dendrou CA, Donnelly P, Dubois B, Fontaine B, Fugger L, Goris A, Gourraud PA, Graetz C, Hemmer B, Hillert J, Kockum I, Leslie S, Lill CM, Martinelli-Boneschi F, Oksenberg JR, Olsson T, Oturai A, Saarela J, Søndergaard HB, Spurkland A, Taylor B, Winkelmann J, Zipp F, Haines JL, Pericak-Vance MA, Spencer CCA, Stewart G, Hafler DA, Ivinson AJ, Harbo HF, Hauser SL, De Jager PL, Compston A, McCauley JL, Sawcer S, McVean G. Class II HLA interactions modulate genetic risk for multiple sclerosis. Nat Genet 2015; 47:1107-1113. [PMID: 26343388 PMCID: PMC4874245 DOI: 10.1038/ng.3395] [Citation(s) in RCA: 242] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 08/12/2015] [Indexed: 01/01/2023]
Abstract
Association studies have greatly refined the understanding of how variation within the human leukocyte antigen (HLA) genes influences risk of multiple sclerosis. However, the extent to which major effects are modulated by interactions is poorly characterized. We analyzed high-density SNP data on 17,465 cases and 30,385 controls from 11 cohorts of European ancestry, in combination with imputation of classical HLA alleles, to build a high-resolution map of HLA genetic risk and assess the evidence for interactions involving classical HLA alleles. Among new and previously identified class II risk alleles (HLA-DRB1*15:01, HLA-DRB1*13:03, HLA-DRB1*03:01, HLA-DRB1*08:01 and HLA-DQB1*03:02) and class I protective alleles (HLA-A*02:01, HLA-B*44:02, HLA-B*38:01 and HLA-B*55:01), we find evidence for two interactions involving pairs of class II alleles: HLA-DQA1*01:01-HLA-DRB1*15:01 and HLA-DQB1*03:01-HLA-DQB1*03:02. We find no evidence for interactions between classical HLA alleles and non-HLA risk-associated variants and estimate a minimal effect of polygenic epistasis in modulating major risk alleles.
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Affiliation(s)
- Loukas Moutsianas
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Luke Jostins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ashley H Beecham
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | | | - Dionysia K Xifara
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Maria Ban
- Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Tejas S Shah
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Nikolaos A Patsopoulos
- Program in Translational NeuroPsychiatric Genomics, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard University and MIT, Cambridge, Massachusetts, USA
| | - Lars Alfredsson
- Institute of Environmental Medicine (IMM), Karolinska Institutet, Stockholm, Sweden
| | - Carl A Anderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Katherine E Attfield
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Sergio E Baranzini
- Department of Neurology, University of California, San Francisco, Sandler Neurosciences Center, San Francisco, California, USA
| | - Jeffrey Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Thomas M C Binder
- HLA Laboratory, Department of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - David Booth
- Westmead Millennium Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Dorothea Buck
- Department of Neurology, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Elisabeth G Celius
- Department of Neurology, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Chris Cotsapas
- Program in Medical and Population Genetics, Broad Institute of Harvard University and MIT, Cambridge, Massachusetts, USA
- Department of Neurology and Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sandra D'Alfonso
- Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Calliope A Dendrou
- Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Peter Donnelly
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Bénédicte Dubois
- Department of Neurosciences, Laboratory for Neuroimmunology, KU Leuven, Leuven, Belgium
| | - Bertrand Fontaine
- INSERM, Université Pierre et Marie Curie, CNRS, Assistance Publique-Hôpitaux de Paris (AP-HP), Département des Maladies du Système Nerveux and UMRS 1127-7225, Institut Cerveau Moelle Spinal Cord and Brain Institute, Pitié-Salpêtrière, Paris, France
| | - Lars Fugger
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - An Goris
- Department of Neurosciences, Laboratory for Neuroimmunology, KU Leuven, Leuven, Belgium
| | - Pierre-Antoine Gourraud
- Department of Neurology, University of California, San Francisco, Sandler Neurosciences Center, San Francisco, California, USA
| | - Christiane Graetz
- Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn2), Johannes Gutenberg University-Medical Center, Mainz, Germany
| | - Bernhard Hemmer
- Department of Neurology, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- German Competence Network Multiple Sclerosis (KKNMS), Munich, Germany
| | - Jan Hillert
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ingrid Kockum
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Stephen Leslie
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Melbourne, Victoria, Australia
- Department of Mathematics and Statistics, University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Christina M Lill
- Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn2), Johannes Gutenberg University-Medical Center, Mainz, Germany
- Platform for Genome Analytics, Institutes of Neurogenetics and Integrative and Experimental Genomics, University of Lübeck, Lübeck, Germany
| | - Filippo Martinelli-Boneschi
- Laboratory of Genetics of Neurological Complex Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
- Department of Neurology, Institute of Experimental Neurology (INSPE), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Jorge R Oksenberg
- Department of Neurology, University of California, San Francisco, Sandler Neurosciences Center, San Francisco, California, USA
| | - Tomas Olsson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Annette Oturai
- Department of Neurology, Danish Multiple Sclerosis Center, Copenhagen University Hospital, Copenhagen, Denmark
| | - Janna Saarela
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Helle Bach Søndergaard
- Department of Neurology, Danish Multiple Sclerosis Center, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne Spurkland
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Bruce Taylor
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, Tasmania, Australia
| | - Juliane Winkelmann
- Department of Neurology, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- Institut für Humangenetik, Technische Universität München, Munich, Germany
- Institut für Humangenetik, Helmholtz Zentrum München, Munich, Germany
- Department of Neurology and Neurological Sciences, Center for Sleep Sciences and Medicine, Stanford University, Stanford, California, USA
| | - Frauke Zipp
- Focus Program Translational Neuroscience (FTN), Rhine Main Neuroscience Network (rmn2), Johannes Gutenberg University-Medical Center, Mainz, Germany
| | - Jonathan L Haines
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Chris C A Spencer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Graeme Stewart
- Westmead Millennium Institute, University of Sydney, Sydney, New South Wales, Australia
| | - David A Hafler
- Program in Medical and Population Genetics, Broad Institute of Harvard University and MIT, Cambridge, Massachusetts, USA
- Department of Neurology and Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Broad Institute of Harvard University and MIT, Cambridge, Massachusetts, USA
| | - Adrian J Ivinson
- Harvard NeuroDiscovery Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Hanne F Harbo
- Department of Neurology, Oslo University Hospital, Ullevål, Oslo, Norway
- University of Oslo, Oslo, Norway
| | - Stephen L Hauser
- Department of Neurology, University of California, San Francisco, Sandler Neurosciences Center, San Francisco, California, USA
| | - Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard University and MIT, Cambridge, Massachusetts, USA
| | - Alastair Compston
- Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Jacob L McCauley
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Stephen Sawcer
- Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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