Abstract
Genome-wide association studies and candidate gene studies in ulcerative colitis have identified 18 susceptibility loci. We conducted a meta-analysis of six ulcerative colitis genome-wide association study datasets, comprising 6,687 cases and 19,718 controls, and followed up the top association signals in 9,628 cases and 12,917 controls. We identified 29 additional risk loci (P < 5 × 10−8), increasing the number of ulcerative colitis–associated loci to 47. After annotating associated regions using GRAIL, expression quantitative trait loci data and correlations with non-synonymous SNPs, we identified many candidate genes that provide potentially important insights into disease pathogenesis, including IL1R2, IL8RA-IL8RB, IL7R, IL12B, DAP, PRDM1, JAK2, IRF5, GNA12 and LSP1. The total number of confirmed inflammatory bowel disease risk loci is now 99, including a minimum of 28 shared association signals between Crohn's disease and ulcerative colitis.
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Change history
11 August 2011
In the version of this article initially published, an affiliation was missing for two authors, Maria Gazouli and Nicholas P. Anagnou. They are also affiliated with the Foundation for Biomedical Research of the Academy of Athens in Athens, Greece. The error has been corrected in the HTML and PDF versions of the article.
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Acknowledgements
In memoriam to Marc Lémann, who dedicated his life to his patients but died too soon.
We thank all the subjects who contributed samples and the physicians and nursing staff who helped with recruitment globally. This study was supported by the German Ministry of Education and Research through the National Genome Research Network, the Popgen biobank and infrastructure support through the Deutsche Forschungsgemeinschaft (DFG) cluster of excellence 'Inflammation at Interfaces'. Italian case collections were supported by the Italian Group for IBD and the Italian Society for Paediatric Gastroenterology, Hepatology and Nutrition. We acknowledge funding provided by the Royal Brisbane and Women's Hospital Foundation, University of Queensland (Ferguson Fellowship), National Health and Medical Research Council, Australia and by the European Community (5th PCRDT). UK case collections were supported by the National Association for Colitis and Crohn's disease, Wellcome Trust, Medical Research Council UK and Peninsular College of Medicine and Dentistry, Exeter. Activities in Sweden were supported by the Swedish Society of Medicine, the Bengt Ihre Foundation, the Karolinska Institutet, the Swedish National Program for IBD Genetics, the Swedish Organization for IBD, the Swedish Medical Research Council, the Soderbergh Foundation and the Swedish Cancer Foundation. Support for genotyping and genetic data analysis was provided by the Agency for Science Technology and Research (A*STAR), Singapore. We are grateful to the funders and investigators of the Epidemiological Investigation of Rheumatoid Arthritis for providing genotype data from healthy Swedish individuals.
The Wellcome Trust Case Control Consortium 2 project was supported by Wellcome Trust grant 083948/Z/07/Z. We also acknowledge the National Institute for Health Research (NIHR) Biomedical Research Centre awards to Guy's & St. Thomas' National Health Service (NHS) Trust, King's College London and to Addenbrooke's Hospital, University of Cambridge School of Clinical Medicine and to the University of Manchester and Central Manchester Foundation Trust. The NIDDK IBD Genetics Consortium 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.). J.H.C. is also funded by the Crohn's and Colitis Foundation of America; S.L.G. by DK069513 and Primary Children's Medical Center Foundation; and J.D.R. by US National Institutes of Health (NIH)/NIDDK grant DK064869. Cedars-Sinai is supported by National Center for Research Resources (NCRR) grant M01-RR00425, NIH/NIDDK grant P01-DK046763, DK 063491 and Cedars-Sinai Medical Center Inflammatory Bowel Disease Research Funds. E.L., D.F. and S.V. are senior clinical investigators for the Funds for Scientific Research (FWO/FNRS) Belgium. S. Brand was supported by Deutsche Forschungsgemeinschaft (DFG BR 1912/5-1) and Else Kröner-Fresenius-Stiftung (P50/05/EKMS05/62). M.C. was supported by the Programme Hospitalier de Recherche Clinique. C.A.A. is supported by Wellcome Trust grant WT091745/Z/10/Z. J.C.B. is supported by Wellcome Trust grant WT089120/Z/09/Z. R.K.W. is supported by a clinical fellowship grant (90.700.281) from the Netherlands Organization for Scientific Research (NWO). C.W. is supported by grants from the Celiac Disease Consortium (BSIK03009) and The Netherlands Organization for Scientific Research (NWO, VICI grant 918.66.620). L.H.v.d.B. acknowledges funding from the Prinses Beatrix Fonds, the Adessium Foundation and the Amyotrophic Lateral Sclerosis Association. L.F. received a Horizon Breakthrough grant from the Netherlands Genomics Initiative (93519031) and a VENI grant from NWO (ZonMW grant 916.10.135). R.J.X. and A.N. are funded by DK83756, AI062773, DK043351 and the Helmsley Foundation.
Replication genotyping was supported by unrestricted grants from Abbott Laboratories Ltd, Giuliani SpA, Shire PLC and Ferring Pharmaceuticals. We thank the 1958 British Birth Cohort and Banco Nacional deADN, Salamanca, Spain, who supplied control DNA samples. The IBSEN study group and the Norwegian Bone Marrow Donor Registry are acknowledged for contributing the Norwegian patient and control populations. The Cardiovascular Health Study (CHS) research reported in this article was supported by contract numbers N01-HC-85079 through N01-HC- 85086, N01-HC-35129, N01 HC-15103, N01 HC-55222, N01-HC-75150, N01-HC-45133, grant numbers U01 HL080295 and R01 HL087652 from the National Heart, Lung, and Blood Institute, with additional contribution from the National Institute of Neurological Disorders and Stroke. A full list of principal CHS investigators and institutions can be found at http://www.chs-nhlbi.org/pi.htm. We thank the members of the Quebec IBD Genetic Consortium, in particular A. Bitton, G. Aumais, E.J. Bernard, A. Cohen, C. Deslandres, R. Lahaie, D. Langelier and P. Paré. Other important contributors are K. Hanigan, N. Huang, P. Webb, D. Whiteman, A. Rutherford, R. Gwilliam, J. Ghori, D. Strachan, W. McCardle, W. Ouwehand, M. Newsky, S. Ehlers, I. Pauselius, K. Holm, C. Sina, M. Regueiro, A. Andriulli and M.C. Renda.
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C.W.L., A.F., K.D.T., J.C.L., M.I., A. Latiano, L.A., L.B., R.N.B., M.B., T.M.B., S. Brand, C.B., J.-F.C., L.A.D., M.D.V., M.D., C.E., R.S.N.F., T.F., D.F., M. Georges, J.G., N.L.G., S.L.G., T.H., N.K.H., J.-P.H., G.J., D.L., I.L., M.L., A. Levine, C. Libioulle, E.L., D.P.M., M.M., C.M., A.N., W.N., R.A.O., L.P., O.P., L.P.-B., J.P., A.P., N.J.P., D.D.P., R. Roberts, R. Russell, P.R., J. Sanderson, M. Sans, P.S., F.S., Y.S., M. Seielstad, A.H.S., S.R.T., L.H.v.d.B., M.V., H.V., T.W., C.W., D.C.W., H.-J.W., C.Y.P., V. Andersen, L.T., M. Gazouli, N.P.A., T.H.K., L.K., J. Sventoraityte, J.C.M., S.K., M.S.S., J.H., J.I.R., C.G.M., A.M.G., R.G., T.A., S.R.B., M.C., J. Satsangi, J.H.C., S.S., M.P., V. Annese, H.H., G.R.-S., R.H.D., S.V., R.K.W. and J.D.R. established DNA collections, recruited patients or assembled phenotypic data. A.F., M.D., P.G., C. Lagacé, R.S., S. Bumpstead, C. Libioulle, D.P.M., G.W.M., L.A.S., Z.Z.Z., M.C., R.H.D. and J.D.R. conducted or supervised laboratory work. C.A.A., G.B., D.E., J.A.B.F., L.F., K.I.M., A.N., R.A.O., R.J.X., M.J.D., J.C.B., R.K.W. and J.D.R. performed or supervised statistical analyses. C.A.A., G.B., C.W.L., G.R.-S., R.H.D., S.V., R.K.W. and J.D.R. drafted the manuscript. All authors read and approved the final manuscript before submission.
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Supplementary information
Supplementary Text and Figures
Supplementary Tables 1, 2, 4–6 and 8 and Supplementary Figures 1–3. (PDF 3143 kb)
Supplementary Table 3a
Cohort specific results for all SNPs listed in Table 1 and Table 2 (XLSX 63 kb)
Supplementary Table 3b
Cohort specific results for all SNPs included in follow-up phase, but failed our thresholds for follow-up (XLSX 38 kb)
Supplementary Table 7
Summary of candidate genes mapping from in silico analysis on the 47 UC loci (XLSX 13 kb)
Supplementary Table 9
Results from the International IBD Genetics Consortium CD and UC meta-analyses for the 99 loci reported for association in CD and/or UC (XLSX 37 kb)
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Anderson, C., Boucher, G., Lees, C. et al. Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet 43, 246–252 (2011). https://doi.org/10.1038/ng.764
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DOI: https://doi.org/10.1038/ng.764
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