Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease (original) (raw)
Accession codes
Data deposits
Data have been deposited in the NCBI database of Genotypes and Phenotypes under accession numbers phs000130.v1.p1 and phs000345.v1.p1. Summary statistics for imputed GWAS are available at http://www.broadinstitute.org/mpg/ricopili/. Summary statistics for the meta-analysis markers are available at http://www.ibdgenetics.org/. The 523 causal gene network Cytoscape file is available on request.
References
- Molodecky, N. A. et al. Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review. Gastroenterology 142, 46–54 (2012)
Google Scholar - Anderson, C. A. et al. Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nature Genet. 43, 246–252 (2011)
Article CAS Google Scholar - Franke, A. et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn’s disease susceptibility loci. Nature Genet. 42, 1118–1125 (2010)
Article CAS Google Scholar - Khor, B., Gardet, A. & Xavier, R. J. Genetics and pathogenesis of inflammatory bowel disease. Nature 474, 307–317 (2011)
Article CAS Google Scholar - Cho, J. H. & Gregersen, P. K. Genomics and the multifactorial nature of human autoimmune disease. N. Engl. J. Med. 365, 1612–1623 (2011)
Article CAS Google Scholar - Cortes, A. & Brown, M. A. Promise and pitfalls of the Immunochip. Arthritis Res. Ther. 13, 101 (2011)
Article Google Scholar - Zuk, O., Hechter, E., Sunyaev, S. R. & Lander, E. S. The mystery of missing heritability: genetic interactions create phantom heritability. Proc. Natl Acad. Sci. USA 109, 1193–1198 (2012)
Article ADS CAS Google Scholar - Raychaudhuri, S. et al. Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. PLoS Genet. 5, e1000534 (2009)
Article Google Scholar - Hindorff, L. A. et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA 106, 9362–9367 (2009)
Article ADS CAS Google Scholar - Notarangelo, L. D. et al. Primary immunodeficiencies: 2009 update. J. Allergy Clin. Immunol. 124, 1161–1178 (2009)
Article CAS Google Scholar - Bustamante, J., Picard, C., Boisson-Dupuis, S., Abel, L. & Casanova, J. L. Genetic lessons learned from X-linked Mendelian susceptibility to mycobacterial diseases. Ann. NY Acad. Sci. 1246, 92–101 (2011)
Article ADS CAS Google Scholar - Patel, S. Y., Doffinger, R., Barcenas-Morales, G. & Kumararatne, D. S. Genetically determined susceptibility to mycobacterial infection. J. Clin. Pathol. 61, 1006–1012 (2008)
Article CAS Google Scholar - Zhang, F. et al. Identification of two new loci at IL23R and RAB32 that influence susceptibility to leprosy. Nature Genet. 43, 1247–1251 (2011)
Article CAS Google Scholar - Holland, S. M. et al. STAT3 mutations in the hyper-IgE syndrome. N. Engl. J. Med. 357, 1608–1619 (2007)
Article CAS Google Scholar - Minegishi, Y. et al. Dominant-negative mutations in the DNA-binding domain of STAT3 cause hyper-IgE syndrome. Nature 448, 1058–1062 (2007)
Article ADS CAS Google Scholar - Glocker, E. O. et al. A homozygous CARD9 mutation in a family with susceptibility to fungal infections. N. Engl. J. Med. 361, 1727–1735 (2009)
Article CAS Google Scholar - Hu, X. et al. Integrating autoimmune risk loci with gene-expression data identifies specific pathogenic immune cell subsets. Am. J. Hum. Genet. 89, 496–506 (2011)
Article CAS Google Scholar - Zhang, B. & Horvath, S. A general framework for weighted gene co-expression network analysis. Stat. Appl. Genet. Mol. Biol. 4, Article 17 (2005)
Article MathSciNet Google Scholar - Greenawalt, D. M. et al. A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort. Genome Res. 21, 1008–1016 (2011)
Article CAS Google Scholar - Emilsson, V. et al. Genetics of gene expression and its effect on disease. Nature 452, 423–428 (2008)
Article ADS CAS Google Scholar - Schadt, E. E. et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol. 6, e107 (2008)
Article Google Scholar - Chen, Y. et al. Variations in DNA elucidate molecular networks that cause disease. Nature 452, 429–435 (2008)
Article ADS CAS Google Scholar - Zhong, H. et al. Liver and adipose expression associated SNPs are enriched for association to type 2 diabetes. PLoS Genet. 6, e1000932 (2010)
Article Google Scholar - Zhu, J. et al. Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations. PLOS Comput. Biol. 3, e69 (2007)
Article ADS MathSciNet Google Scholar - Lewis, S. J., Baker, I. & Davey Smith, G. Meta-analysis of vitamin D receptor polymorphisms and pulmonary tuberculosis risk. Int. J. Tuberc. Lung Dis. 9, 1174–1177 (2005)
CAS PubMed Google Scholar - Li, X. et al. SLC11A1 (NRAMP1) polymorphisms and tuberculosis susceptibility: updated systematic review and meta-analysis. PLoS ONE 6, e15831 (2011)
Article ADS CAS Google Scholar - Kumar, D. et al. Genome-wide analysis of the host intracellular network that regulates survival of Mycobacterium tuberculosis. Cell 140, 731–743 (2010)
Article CAS Google Scholar - Glocker, E. O. et al. Infant colitis–it’s in the genes. Lancet 376, 1272 (2010)
Article Google Scholar - Franke, A. et al. Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility. Nature Genet. 40, 1319–1323 (2008)
Article CAS Google Scholar - Bhattacharjee, A., Pal, S., Feldman, G. M. & Cathcart, M. K. Hck is a key regulator of gene expression in alternatively activated human monocytes. J. Biol. Chem. 286, 36709–36723 (2011)
Article CAS Google Scholar
Acknowledgements
We thank all the subjects who contributed samples and the physicians and nursing staff who helped with recruitment globally. UK case collections were supported by the National Association for Colitis and Crohn’s disease; Wellcome Trust grant 098051 (L.J., C.A.A., J.C.B.); Medical Research Council UK; the Catherine McEwan Foundation; an NHS Research Scotland career fellowship (R.K.R.); Peninsula College of Medicine and Dentistry, Exeter; the National Institute for Health Research, through the Comprehensive Local Research Network, and through Biomedical Research Centre awards to Guy’s & Saint Thomas’ National Health Service Trust, King’s College London, Addenbrooke’s Hospital, University of Cambridge School of Clinical Medicine and to the University of Manchester and Central Manchester Foundation Trust. The British 1958 Birth Cohort DNA collection was funded by Medical Research Council grant G0000934 and Wellcome Trust grant 068545/Z/02, and the UK National Blood Service controls by the Wellcome Trust. The Wellcome Trust Case Control Consortium projects were supported by Wellcome Trust grants 083948/Z/07/Z, 085475/B/08/Z and 085475/Z/08/Z. North American collections and data processing were supported by funds to the National Institute of Diabetes, Digestive and Kidney diseases (NIDDK) IBD Genetics Consortium, which is funded by the following grants: DK062431 (S.R.B.), DK062422 (J.H.C.), DK062420 (R.H.D.), DK062432 (J.D.R.), DK062423 (M.S.S.), DK062413 (D.P.M.), DK076984 (M.J.D.), DK084554 (M.J.D. and D.P.M.) and DK062429 (J.H.C.). Additional funds were provided by funding to J.H.C. (DK062429-S1 and Crohn’s & Colitis Foundation of America, Senior Investigator Award (5-2229)) and R.H.D. (CA141743). K.Y.H. is supported by the National Institutes of Health (NIH) MSTP TG T32GM07205 training award. Cedars-Sinai is supported by USPHS grant PO1DK046763 and the Cedars-Sinai F. Widjaja Inflammatory Bowel and Immunobiology Research Institute Research Funds, National Center for Research Resources (NCRR) grant M01-RR00425, UCLA/Cedars-Sinai/Harbor/Drew Clinical and Translational Science Institute (CTSI) Grant (UL1 TR000124-01), the Southern California Diabetes and Endocrinology Research Grant (DERC) (DK063491), The Helmsley Foundation (D.P.M.) and the Crohn's and Colitis Foundation of America (D.P.M.). R.J.X. and A.N.A. are funded by DK83756, AI062773, DK043351 and the Helmsley Foundation. The Netherlands Organization for Scientific Research supported R.K.W. with a clinical fellowship grant (90.700.281) and C.W. (VICI grant 918.66.620). C.W. is also supported by the Celiac Disease Consortium (BSIK03009). This study was also supported by the German Ministry of Education and Research through the National Genome Research Network, the Popgen biobank, through the Deutsche Forschungsgemeinschaft (DFG) cluster of excellence ‘Inflammation at Interfaces’ and DFG grant no. FR 2821/2-1. S.B. was supported by DFG BR 1912/6-1 and the Else Kröner-Fresenius-Stiftung (Else Kröner-Exzellenzstipendium 2010_EKES.32). Italian case collections were supported by the Italian Group for IBD and the Italian Society for Paediatric Gastroenterology, Hepatology and Nutrition and funded by the Italian Ministry of Health GR-2008-1144485. Activities in Sweden were supported by the Swedish Society of Medicine, Ihre Foundation, Örebro University Hospital Research Foundation, Karolinska Institutet, the Swedish National Program for IBD Genetics, the Swedish Organization for IBD, and the Swedish Medical Research Council. D.F. and S.V. are senior clinical investigators for the Funds for Scientific Research (FWO/FNRS) Belgium. We acknowledge a grant from Viborg Regional Hospital, Denmark. V. Andersen was supported by SHS Aabenraa, Denmark. We acknowledge funding provided by the Royal Brisbane and Women’s Hospital Foundation, National Health and Medical Research Council, Australia and by the European Community (5th PCRDT). We acknowledge the following groups that provided biological samples or data for this study: the Inflammatory Bowel in South Eastern Norway (IBSEN) study group, the Norwegian Bone Marrow Donor Registry (NMBDR), the Avon Longitudinal Study of Parents and Children, the Human Biological Data Interchange and Diabetes UK, and Banco Nacional de ADN, Salamanca. This research also uses resources provided by the Type 1 Diabetes Genetics Consortium, a collaborative clinical study sponsored by the NIDDK, National Institute of Allergy and Infectious Diseases (NIAID), National Human Genome Research Institute (NHGRI), National Institute of Child Health and Human Development (NICHD), and Juvenile Diabetes Research Foundation (JDRF) and supported by U01 DK062418. The KORA study was initiated and financed by the Helmholtz Zentrum München – German Research Center for Environmental Health, which is funded by the German Federal Ministry of Education and Research (BMBF) and by the State of Bavaria. KORA research was supported within the Munich Center of Health Sciences (MC Health), Ludwig-Maximilians-Universität, as part of LMUinnovativ.
Author information
Author notes
- Luke Jostins, Stephan Ripke, Jeffrey C. Barrett and Judy H Cho: These authors contributed equally to this work.
Authors and Affiliations
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK.,
Luke Jostins, Carl A. Anderson & Jeffrey C. Barrett - Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, 02114, Massachusetts, USA
Stephan Ripke & Mark J. Daly - Broad Institute of MIT and Harvard, Cambridge, 02142, Massachusetts, USA
Stephan Ripke & Mark J. Daly - Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen 9700 RB, The Netherlands.,
Rinse K. Weersma & Dirk De Jong - Division of Gastroenterology, Department of Medicine, Hepatology and Nutrition, University of Pittsburgh School of Medicine, Pittsburgh, 15261, Pennsylvania, USA
Richard H. Duerr, Leonard Baidoo, Karin Fransen & Miguel Regueiro - Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, 15261, Pennsylvania, USA
Richard H. Duerr - F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, 90048, California, USA
Dermot P. McGovern, Stephan R. Targan & Kent D. Taylor - Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, 90048, California, USA
Dermot P. McGovern, Talin Haritunians, Jerome I. Rotter & Kent D. Taylor - Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520, USA.,
Ken Y. Hui & Judy H Cho - Inflammatory Bowel Disease Research Group, Addenbrooke’s Hospital, University of Cambridge, Cambridge CB2 0QQ, UK.,
James C. Lee & Miles Parkes - Department of Health Studies, University of Chicago, Chicago, 60637, Illinois, USA
L. Philip Schumm - Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut 06520, USA.,
Yashoda Sharma, Kaida Ning, Clara Abraham, Matija Hedl & Judy H Cho - Center for Human Genetic Research, Massachusetts General Hospital, Harvard Medical School, Boston, 02114, Massachusetts, USA
Jonah Essers - University of Maribor, Faculty of Medicine, Center for Human Molecular Genetics and Pharmacogenomics, Maribor 2000, Slovenia.,
Mitja Mitrovic & Uros Potocnik - Department of Genetics, University Medical Center Groningen, Groningen 9700 RB, The Netherlands.,
Mitja Mitrovic - Department of Clinical and Experimental Medicine, Gastroenterology section, KU Leuven, Leuven 3000, Belgium.,
Isabelle Cleynen & Severine Vermeire - Unit of Animal Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) and Faculty of Veterinary Medicine, University of Liège, Liège 4000, Belgium.,
Emilie Theatre & Michel Georges - Division of Gastroenterology, Centre Hospitalier Universitaire, Université de Liège, Liège 4000, Belgium.,
Emilie Theatre & Edouard Louis - Department of Medical and Molecular Genetics, Division of Genetics and Molecular Medicine, King’s College London School of Medicine, Guy’s Hospital, London SE1 9RT, UK.,
Sarah L. Spain, Natalie J. Prescott & Christopher G. Mathew - Division of Rheumatology Immunology and Allergy, Brigham and Women’s Hospital, Boston, 02115, Massachusetts, USA
Soumya Raychaudhuri & Xinli Hu - Program in Medical and Population Genetics, Broad Institute, Cambridge, 02142, Massachusetts, USA
Soumya Raychaudhuri - Division of Genetics, Brigham and Women’s Hospital, Boston, 02115, Massachusetts, USA
Soumya Raychaudhuri - Université de Montréal and the Montreal Heart Institute, Research Center, Montréal, Québec H1T 1C8, Canada.,
Philippe Goyette, Gabrielle Boucher & John D. Rioux - Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA.,
Zhi Wei - Department of Gastroenterology & Hepatology, Digestive Disease Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,
Jean-Paul Achkar - Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, 44195, Ohio, USA
Jean-Paul Achkar - Peninsula College of Medicine and Dentistry, Exeter EX1 2LU, UK.,
Tariq Ahmad - Department of Gastroenterology, Erasmus Hospital, Free University of Brussels, Brussels, 1070 Belgium.,
Leila Amininejad & Denis Franchimont - Massachusetts General Hospital, Harvard Medical School, Gastroenterology Unit, Boston, 02114, Massachusetts, USA
Ashwin N. Ananthakrishnan, Kathy L. Devaney & Ramnik J. Xavier - Medical Department, Viborg Regional Hospital, Viborg 8800, Denmark.,
Vibeke Andersen - Department of Gastroenterology and Hepatology, Inflammatory Bowel Disease Service, Royal Adelaide Hospital, and School of Medicine, University of Adelaide, Adelaide 5000, Australia.,
Jane M. Andrews - Institute of Clinical Chemistry, Christian-Albrechts-University, Kiel 24105, Germany.,
Tobias Balschun, David Ellinghaus, Stefan Schreiber & Andre Franke - Department of Gastroenterology and Hepatology, Flinders Medical Centre and School of Medicine, Flinders University, Adelaide 5000, Australia.,
Peter A. Bampton - Division of Gastroenterology, McGill University Health Centre, Royal Victoria Hospital, Montréal, Québec H3A 1A1, Canada.,
Alain Bitton & Jürgen Glas - Department of Medicine II, University Hospital Munich-Grosshadern, Ludwig-Maximilians-University, Munich 80336, Germany.,
Stephan Brand - Department of Gastroenterology, Charité, Campus Mitte, Universitätsmedizin Berlin, Berlin 10117, Germany.,
Carsten Büning - Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York City, 10029, New York, USA
Ariella Cohain, Bin Zhang & Eric E. Schadt - Department of Genomics, Life & Brain Center, University Hospital Bonn, Bonn 53012, Germany.,
Sven Cichon - Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm 14 183, Sweden.,
Mauro D’Amato - Department of Pediatrics, Cedars Sinai Medical Center, Los Angeles, 90048, California, USA
Marla Dubinsky - Department of Gastroenterology, Torbay Hospital, Torbay, Devon TQ2 7AA, UK.,
Cathryn Edwards - School of Medical Sciences, Faculty of Medical & Health Sciences, The University of Auckland, Auckland 1142, New Zealand.,
Lynnette R. Ferguson & Angharad R. Morgan - Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen T9700 RB, The Netherlands.,
Karin Fransen & Cisca Wijmenga - Department of Medicine, University of Otago, Christchurch 8140, New Zealand.,
Richard Gearry - Department of Gastroenterology, Christchurch Hospital, Christchurch 8011, New Zealand.,
Richard Gearry - Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany.,
Christian Gieger - St Mark’s Hospital, Watford Road, Harrow, Middlesex HA1 3UJ, UK.,
Ailsa Hart - Nottingham Digestive Diseases Centre, Queens Medical Centre, Nottingham NG7 1AW, UK.,
Chris Hawkey - Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo 0424, Norway.,
Tom H. Karlsen - Department of Gastroenterology, Kaunas University of Medicine, Kaunas 44307, Lithuania.,
Limas Kupcinskas & Jurgita Sventoraityte - Department of Pediatrics, Emory University School of Medicine, Atlanta, 30322, Georgia, USA
Subra Kugathasan - Unit of Gastroenterology, Istituto di Ricovero e Cura a Carattere Scientifico-Casa Sollievo della Sofferenza (IRCCS-CSS) Hospital, San Giovanni Rotondo 71013, Italy.,
Anna Latiano, Orazio Palmieri & Vito Annese - Department of Gastroenterology and Hepatology, Ghent University Hospital, Ghent 9000, Belgium.,
Debby Laukens & Martine De Vos - School of Medicine and Pharmacology, The University of Western Australia, Fremantle, Western Australia 6009, Australia.,
Ian C. Lawrance - Gastrointestinal Unit, Molecular Medicine Centre, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK.,
Charlie W. Lees & Jack Satsangi - Department of Gastroenterology, The Townsville Hospital, Townsville, 4810, Queensland, Australia
Gillian Mahy - Institute of Human Genetics, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.,
John Mansfield - Department of Medicine, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK.,
Craig Mowat - Genetic Medicine, MAHSC, University of Manchester, Manchester M13 9PL, UK.,
William Newman - Department of Gastroenterology, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.,
Cyriel Y. Ponsioen - University of Maribor, Faculty for Chemistry and Chemical Engineering, Maribor 2000, Slovenia.,
Uros Potocnik - Royal Hospital for Sick Children, Paediatric Gastroenterology and Nutrition, Glasgow G3 8SJ, UK.,
Richard K. Russell & David C. Wilson - Department of Gastroenterology, Guy’s & St Thomas’ NHS Foundation Trust, St Thomas’ Hospital, London SE1 7EH, UK.,
Jeremy D. Sanderson - Department of Gastroenterology, Hospital Clinic/Institut d’Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
Miquel Sans - Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBER-EHD), Barcelona 08036, Spain.,
Miquel Sans - Department for General Internal Medicine, Christian-Albrechts-University, Kiel, Kiel 24118, Germany.,
Stefan Schreiber & Sebastian Zeissig - Inflammatory Bowel Diseases, Genetics and Computational Biology, Queensland Institute of Medical Research, Brisbane 4029, Australia.,
Lisa A. Simms & Graham Radford-Smith - Norfolk and Norwich University Hospital, Norwich NR4 7UY, UK.,
Mark Tremelling - Department of Gastroenterology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands.,
Hein W. Verspaget - Child Life and Health, University of Edinburgh, Edinburgh, Scotland EH9 1UW, UK.,
David C. Wilson - Institute of Human Genetics and Department of Neurology, Technische Universität München, Munich 80336, Germany.,
Juliane Winkelmann - Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, 02114, Massachusetts, USA
Ramnik J. Xavier - Department of Biostatistics, School of Public Health, Yale University, New Haven, Connecticut 06520, USA.,
Clarence K. Zhang & Hongyu Zhao - Mount Sinai Hospital Inflammatory Bowel Disease Centre, University of Toronto, Toronto, Ontario M5G 1X5, Canada.,
Mark S. Silverberg - Azienda Ospedaliero Universitaria (AOU) Careggi, Unit of Gastroenterology SOD2, Florence 50134, Italy.,
Vito Annese - Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, 19104, Pennsylvania, USA
Hakon Hakonarson - Department of Pediatrics, Center for Pediatric Inflammatory Bowel Disease, The Children’s Hospital of Philadelphia, Philadelphia, 19104, Pennsylvania, USA
Hakon Hakonarson - Department of Medicine, and Department of Epidemiology, Meyerhoff Inflammatory Bowel Disease Center, School of Medicine, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, 21205, Maryland, USA
Steven R. Brant - Department of Gastroenterology, Royal Brisbane and Women’s Hospital, and School of Medicine, University of Queensland, Brisbane 4029, Australia
Graham Radford-Smith - Department of Gastroenterology, University Hospital Leuven, Leuven 3000, Belgium,
Severine Vermeire
Authors
- Luke Jostins
You can also search for this author inPubMed Google Scholar - Stephan Ripke
You can also search for this author inPubMed Google Scholar - Rinse K. Weersma
You can also search for this author inPubMed Google Scholar - Richard H. Duerr
You can also search for this author inPubMed Google Scholar - Dermot P. McGovern
You can also search for this author inPubMed Google Scholar - Ken Y. Hui
You can also search for this author inPubMed Google Scholar - James C. Lee
You can also search for this author inPubMed Google Scholar - L. Philip Schumm
You can also search for this author inPubMed Google Scholar - Yashoda Sharma
You can also search for this author inPubMed Google Scholar - Carl A. Anderson
You can also search for this author inPubMed Google Scholar - Jonah Essers
You can also search for this author inPubMed Google Scholar - Mitja Mitrovic
You can also search for this author inPubMed Google Scholar - Kaida Ning
You can also search for this author inPubMed Google Scholar - Isabelle Cleynen
You can also search for this author inPubMed Google Scholar - Emilie Theatre
You can also search for this author inPubMed Google Scholar - Sarah L. Spain
You can also search for this author inPubMed Google Scholar - Soumya Raychaudhuri
You can also search for this author inPubMed Google Scholar - Philippe Goyette
You can also search for this author inPubMed Google Scholar - Zhi Wei
You can also search for this author inPubMed Google Scholar - Clara Abraham
You can also search for this author inPubMed Google Scholar - Jean-Paul Achkar
You can also search for this author inPubMed Google Scholar - Tariq Ahmad
You can also search for this author inPubMed Google Scholar - Leila Amininejad
You can also search for this author inPubMed Google Scholar - Ashwin N. Ananthakrishnan
You can also search for this author inPubMed Google Scholar - Vibeke Andersen
You can also search for this author inPubMed Google Scholar - Jane M. Andrews
You can also search for this author inPubMed Google Scholar - Leonard Baidoo
You can also search for this author inPubMed Google Scholar - Tobias Balschun
You can also search for this author inPubMed Google Scholar - Peter A. Bampton
You can also search for this author inPubMed Google Scholar - Alain Bitton
You can also search for this author inPubMed Google Scholar - Gabrielle Boucher
You can also search for this author inPubMed Google Scholar - Stephan Brand
You can also search for this author inPubMed Google Scholar - Carsten Büning
You can also search for this author inPubMed Google Scholar - Ariella Cohain
You can also search for this author inPubMed Google Scholar - Sven Cichon
You can also search for this author inPubMed Google Scholar - Mauro D’Amato
You can also search for this author inPubMed Google Scholar - Dirk De Jong
You can also search for this author inPubMed Google Scholar - Kathy L. Devaney
You can also search for this author inPubMed Google Scholar - Marla Dubinsky
You can also search for this author inPubMed Google Scholar - Cathryn Edwards
You can also search for this author inPubMed Google Scholar - David Ellinghaus
You can also search for this author inPubMed Google Scholar - Lynnette R. Ferguson
You can also search for this author inPubMed Google Scholar - Denis Franchimont
You can also search for this author inPubMed Google Scholar - Karin Fransen
You can also search for this author inPubMed Google Scholar - Richard Gearry
You can also search for this author inPubMed Google Scholar - Michel Georges
You can also search for this author inPubMed Google Scholar - Christian Gieger
You can also search for this author inPubMed Google Scholar - Jürgen Glas
You can also search for this author inPubMed Google Scholar - Talin Haritunians
You can also search for this author inPubMed Google Scholar - Ailsa Hart
You can also search for this author inPubMed Google Scholar - Chris Hawkey
You can also search for this author inPubMed Google Scholar - Matija Hedl
You can also search for this author inPubMed Google Scholar - Xinli Hu
You can also search for this author inPubMed Google Scholar - Tom H. Karlsen
You can also search for this author inPubMed Google Scholar - Limas Kupcinskas
You can also search for this author inPubMed Google Scholar - Subra Kugathasan
You can also search for this author inPubMed Google Scholar - Anna Latiano
You can also search for this author inPubMed Google Scholar - Debby Laukens
You can also search for this author inPubMed Google Scholar - Ian C. Lawrance
You can also search for this author inPubMed Google Scholar - Charlie W. Lees
You can also search for this author inPubMed Google Scholar - Edouard Louis
You can also search for this author inPubMed Google Scholar - Gillian Mahy
You can also search for this author inPubMed Google Scholar - John Mansfield
You can also search for this author inPubMed Google Scholar - Angharad R. Morgan
You can also search for this author inPubMed Google Scholar - Craig Mowat
You can also search for this author inPubMed Google Scholar - William Newman
You can also search for this author inPubMed Google Scholar - Orazio Palmieri
You can also search for this author inPubMed Google Scholar - Cyriel Y. Ponsioen
You can also search for this author inPubMed Google Scholar - Uros Potocnik
You can also search for this author inPubMed Google Scholar - Natalie J. Prescott
You can also search for this author inPubMed Google Scholar - Miguel Regueiro
You can also search for this author inPubMed Google Scholar - Jerome I. Rotter
You can also search for this author inPubMed Google Scholar - Richard K. Russell
You can also search for this author inPubMed Google Scholar - Jeremy D. Sanderson
You can also search for this author inPubMed Google Scholar - Miquel Sans
You can also search for this author inPubMed Google Scholar - Jack Satsangi
You can also search for this author inPubMed Google Scholar - Stefan Schreiber
You can also search for this author inPubMed Google Scholar - Lisa A. Simms
You can also search for this author inPubMed Google Scholar - Jurgita Sventoraityte
You can also search for this author inPubMed Google Scholar - Stephan R. Targan
You can also search for this author inPubMed Google Scholar - Kent D. Taylor
You can also search for this author inPubMed Google Scholar - Mark Tremelling
You can also search for this author inPubMed Google Scholar - Hein W. Verspaget
You can also search for this author inPubMed Google Scholar - Martine De Vos
You can also search for this author inPubMed Google Scholar - Cisca Wijmenga
You can also search for this author inPubMed Google Scholar - David C. Wilson
You can also search for this author inPubMed Google Scholar - Juliane Winkelmann
You can also search for this author inPubMed Google Scholar - Ramnik J. Xavier
You can also search for this author inPubMed Google Scholar - Sebastian Zeissig
You can also search for this author inPubMed Google Scholar - Bin Zhang
You can also search for this author inPubMed Google Scholar - Clarence K. Zhang
You can also search for this author inPubMed Google Scholar - Hongyu Zhao
You can also search for this author inPubMed Google Scholar - Mark S. Silverberg
You can also search for this author inPubMed Google Scholar - Vito Annese
You can also search for this author inPubMed Google Scholar - Hakon Hakonarson
You can also search for this author inPubMed Google Scholar - Steven R. Brant
You can also search for this author inPubMed Google Scholar - Graham Radford-Smith
You can also search for this author inPubMed Google Scholar - Christopher G. Mathew
You can also search for this author inPubMed Google Scholar - John D. Rioux
You can also search for this author inPubMed Google Scholar - Eric E. Schadt
You can also search for this author inPubMed Google Scholar - Mark J. Daly
You can also search for this author inPubMed Google Scholar - Andre Franke
You can also search for this author inPubMed Google Scholar - Miles Parkes
You can also search for this author inPubMed Google Scholar - Severine Vermeire
You can also search for this author inPubMed Google Scholar - Jeffrey C. Barrett
You can also search for this author inPubMed Google Scholar - Judy H Cho
You can also search for this author inPubMed Google Scholar
Consortia
The International IBD Genetics Consortium (IIBDGC)
Contributions
R.K.W., R.H.D., D.P.M., C.G.M., J.D.R., E.E.S., M.J.D., A.F., M.P. and S.V. contributed equally to the manuscript. J.H.C., J.C.B., R.K.W., R.H.D., D.P.M., A.F., M.P., C.G.M., J.D.R., S.V., M.D.A. and V. Annese conceived, designed and managed the study and managed the funding. J.H.C., J.C.B., L.J., S. Ripke, R.K.W., R.H.D., D.P.M., M.J.D., M.P. and C.G.M. were involved in manuscript preparation. J.H.C., J.C.B., L.J., S. Ripke, R.K.W., K.Y.H., C.A.A., J.E., K.N., S.L.S., S. Raychaudhuri, Z.W., C.A., A.C., G.B., M.H., X.H., B.Z., C.K.Z., H.Z., J.D.R., E.E.S. and M.J.D. performed or supervised statistical and computational analyses. R.K.W., R.H.D., D.P.M., J.C.L., L.P.S., Y.S., P.G., J.-P.A., T.A., L.A., A.N.A., V. Andersen, J.M.A., L.B., P.A.B., A.B., S.B., C.B., S.C., M.D.A., D.D.J., K.L.D., M.D., C.E., L.R.F., D.F., M.G., C.G., R.G., J.G., A.H., C.H., T.H.K., L.K., S.K., A.L., D.L., E.L., I.C.L., C.W.L., A.R.M., C.M., G.M., J.M., W.N., O.P., C.Y.P., U.P., N.J.P., M.R., J.I.R., R.K.R., J.D.S., M.S., J. Satsangi, S.S., L.A.S., J. Sventoraityte, S.R.T., M.T., H.W.V., M.D.V., C.W., D.C.W., J.W., R.J.X., S.Z., M.S.S., V. Annese, H.H., IIBDGC, S.R.B., J.D.R., G.R.S., C.G.M., A.F., M.P., S.V. and J.H.C. were involved in study subject recruitment and assembling phenotypic data. R.K.W., R.H.D., D.P.M., L.P.S., Y.S., M.M., I.C., E.T., T.B., D.E., K.F., T.H., K.D.T., C.G.M., A.F., M.P. and J.H.C. established DNA collections, genotyping and data management. All authors read and approved the final manuscript before submission.
Corresponding author
Correspondence toJudy H Cho.
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Additional information
Lists of participants and their affiliations appear in the Supplementary Information.
Supplementary information
Supplementary Information
This file contains Supplementary Text, Supplementary Figures 1-12, full legends for Supplementary Tables 1-6, Supplementary References and a list of IBD Genetics Consortium members – see Supplementary Contents for details. (PDF 6835 kb)
Supplementary Tables
This zipped files contains Supplementary Tables 1-6 as follows: 1 shows the GWAS and Immunochip samples used in the study; 2 contains complete details of 163 IBD loci; 3 contains details of disease overlaps with IMD, PID and MSMD described in section 2 of the methods; 4 contains detailed enrichment statistics for all GO terms and canonical pathways; 5 contains the signals of selection at IBD loci; 6 shows enrichment scores for genes in IBD loci within co-expression modules. Supplementary Table 2, which is contained in this zipped file, has been replaced, as there was an error in the original file. In the ‘Detailed assoc stats’ tab, the ‘IC risk’ and ‘IC_nonrisk’ column labels were inadvertently switched. In addition, clarification of the cohort used to determine the odds ratio (OR) shown in the ‘Detailed assoc stats’ and ‘Main Table’ tabs has been included. This file was replaced online on 31 January 2013. (ZIP 356 kb)
Supplementary Data
This zipped file is a Cytoscape file for the macrophage enriched, omental adipose Bayesian network. (ZIP 722 kb)
PowerPoint slides
Rights and permissions
About this article
Cite this article
Jostins, L., Ripke, S., Weersma, R. et al. Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease.Nature 491, 119–124 (2012). https://doi.org/10.1038/nature11582
- Received: 17 May 2012
- Accepted: 12 September 2012
- Published: 31 October 2012
- Issue Date: 01 November 2012
- DOI: https://doi.org/10.1038/nature11582