Fine-mapping inflammatory bowel disease loci to single-variant resolution
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Abstract
Inflammatory bowel diseases are chronic gastrointestinal inflammatory disorders that affect millions of people worldwide. Genome-wide association studies have identified 200 inflammatory bowel disease-associated loci, but few have been conclusively resolved to specific functional variants. Here we report fine-mapping of 94 inflammatory bowel disease loci using high-density genotyping in 67,852 individuals. We pinpoint 18 associations to a single causal variant with greater than 95% certainty, and an additional 27 associations to a single variant with greater than 50% certainty. These 45 variants are significantly enriched for protein-coding changes (n = 13), direct disruption of transcription-factor binding sites (n = 3), and tissue-specific epigenetic marks (n = 10), with the last category showing enrichment in specific immune cells among associations stronger in Crohn's disease and in gut mucosa among associations stronger in ulcerative colitis. The results of this study suggest that high-resolution fine-mapping in large samples can convert many discoveries from genome-wide association studies into statistically convincing causal variants, providing a powerful substrate for experimental elucidation of disease mechanisms.
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Complex traits are highly polygenic, meaning most prediction power comes from small effects that do not meet genome-wide significance and/or cannot be fine-mapped, even in many of the best-powered GWAS to date.
“This is because complex traits are highly polygenic, meaning most of our prediction power comes from small effects that do not meet genome-wide significance and/or cannot be fine-mapped, even in many of the best-powered GWAS to date42.”
From Clinical use of current polygenic risk scores may exacerbate health disparities (2019) · cites this paper as [42]
The Methods section on confounders reports a polygenic signal in the IBD data, and Extended Data Figure 1 says fine-mapping power increases with association significance. The paper does not establish that most predictive power across complex traits comes from small effects below genome-wide significance or from effects that cannot be fine-mapped, even in well-powered GWAS. (LLM, conf=0.83)
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- Authors
- International Inflammatory Bowel Disease Genetics Consortium, Huang, H., Fang, M., Jostins, L., Umićević Mirkov, M., Boucher, G., Anderson, C. A., Andersen, V., Cleynen, I., Cortes, A., Crins, F., D’Amato, M., Deffontaine, V., Dmitrieva, J., Docampo, E., Elansary, M., Farh, K. K.-H., Franke, A., Gori, A.-S., Goyette, P., Halfvarson, J., Haritunians, T., Knight, J., Lawrance, I. C., Lees, C. W., Louis, E., Mariman, R., Meuwissen, T., Mni, M., Momozawa, Y., Parkes, M., Spain, S. L., Théâtre, E., Trynka, G., Satsangi, J., van Sommeren, S., Vermeire, S., Xavier, R. J., Weersma, R. K., Duerr, R. H., Mathew, C. G., Rioux, J. D., McGovern, D. P. B., Cho, J. H., Georges, M., Daly, M. J., & Barrett, J. C.
- Affiliations
- Broad Institute (US)
- University of Liège (BE)
- Centre for Human Genetics (GB)
- Montreal Heart Institute (CA)
- Wellcome Sanger Institute (GB)
- University of Southern Denmark (DK)
- KU Leuven (BE)
- Ikerbasque (ES)
- Örebro University (SE)
- Cedars-Sinai Medical Center (US)
- Lancaster University (GB)
- St John of God Subiaco Hospital (AU)
- Western General Hospital (GB)
- Norwegian University of Life Sciences (NO)
- Addenbrooke's Hospital (GB)
- University Medical Center Groningen (NL)
- University of Pittsburgh (US)
- King's College London (GB)
- Yale University (US)
- Corresponding author
- Huang, Hailiang
- Georges, Michel
- Daly, Mark J.
- Barrett, Jeffrey C.
- ORCID
- Huang, Hailiang
- Fang, Ming
- Boucher, Gabrielle
- Anderson, Carl A.
- Andersen, Vibeke
- Cleynen, Isabelle
- D’Amato, Mauro
- Dmitrieva, Julia
- Elansary, Mahmoud
- Farh, Kyle Kai-How
- Halfvarson, Jonas
- Haritunians, Talin
- Knight, Jo
- Lees, Charlie W.
- Louis, Edouard
- Mariman, Rob
- Meuwissen, Theo
- Momozawa, Yukihide
- Parkes, Miles
- Spain, Sarah L.
- Trynka, Gosia
- Xavier, Ramnik J.
- Weersma, Rinse K.
- Duerr, Richard H.
- Mathew, Christopher G.
- Rioux, John D.
- McGovern, Dermot P. B.
- Cho, Judy H.
- Georges, Michel
- Daly, Mark J.
- Barrett, Jeffrey C.
- Venue
- Nature
- Published
- 2017-06-28
- Volume
- 547
- Issue
- 7662
- Pages
- 173-178
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC5511510
- OpenAlex
- W2724938313
- Cited by
- 611
- References
- 64
- Citations by year
- 2026: 31 · 2025: 44 · 2024: 76 · 2023: 82 · 2022: 63 · 2021: 73 · 2020: 74 · 2019: 81 · 2018: 55 · 2017: 22 · 2016: 8 · 2015: 1
- FWCI
- 42.30
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- UWA Profiles and Research Repository (UWA) (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, other-oa)
- Lancaster EPrints (Lancaster University) (acceptedVersion)
- Research Portal (King's College London) (acceptedVersion, cc-by-nc)
- University of Southern Denmark Research Portal (University of Southern Denmark) (acceptedVersion, other-oa)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- Lirias (KU Leuven) (submittedVersion)
- Open Repository and Bibliography (University of Liège) (submittedVersion, other-oa)
- ORBi (University of Liège) (submittedVersion, other-oa)
- Apollo (University of Cambridge) (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
- Apollo
- Funders
- Crohn's and Colitis Foundation of America (DK062422)
- Leona M. and Harry B. Helmsley Charitable Trust (2015PG-IBD001)
- University of Pittsburgh
- Genome Canada (GPH‐129341)
- Wellcome Trust (098759/Z/12/Z, 098759, 098051)
- Crohn's and Colitis Foundation (IBD-0318R-2)
- Génome Québec
- Kennedy Trust for Rheumatology Research (KENN151613)
- National Institute for Health and Care Research (129341)
- King's College London
- European Commission (305479)
- Deutsche Forschungsgemeinschaft (01ZX1306A)
- Bundesministerium für Bildung und Forschung (01ZX1306A)
- Fonds De La Recherche Scientifique - FNRS
- Belgian Federal Science Policy Office (P7/43)
- Fédération Wallonie-Bruxelles
- Örebro Universitet
- Crohn's and Colitis UK (M14-5)
- Vetenskapsrådet
- Fonds Léon Fredericq
- Universitetssjukhuset Örebro
- Exzellenzclusters Entzündungsforschung
- Walloon excellence in life sciences and biotechnology
- National Institutes of Health (5r01dk092235-06)
- Canadian Institutes of Health Research (102170, 102170_1)
- Medical Research Council (MR/M00533X/1)
- National Cancer Institute (R01CA141743)
- National Institute of Allergy and Infectious Diseases (U01AI067068)
- National Institute of Diabetes and Digestive and Kidney Diseases (P30DK 433-51, P01DK046763, DK062429, DK062413, DK092235, R01-DK092235, DK064869, DK062422, DK062432, R01DK064869, R01DK106593, U01DK062420, U01DK062429, U24DK062429, U01DK062413, U01DK062422, U01DK062432, P30DK043351)
- National Institute of Dental and Craniofacial Research (U54DE023789)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Inflammatory Bowel Disease
- Health Sciences › Medicine › Pathology and Forensic Medicine › Multiple Sclerosis Research Studies
- Keywords
- inflammatory bowel disease, Crohn's disease, ulcerative colitis, fine mapping, causal variant identification, high-density genotyping, transcription factor binding sites, immune cells, intestinal mucosa, protein-coding variants, disease susceptibility loci
- MeSH terms
- Adolescent, Adult, Aged, Aged, 80 and over, Binding Sites, Chromatin, Colitis, Ulcerative, Crohn Disease, Female, Genotype, Humans, Male, Middle Aged, Transcription Factors, Genetic Variation, Inflammatory Bowel Diseases, Linkage Disequilibrium, Genetic Predisposition to Disease, Quantitative Trait Loci, Epigenesis, Genetic, Smad3 Protein, Genome-Wide Association Study, Young Adult
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