Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations
Open accessAbstract
Rinse Weersma, Carl Anderson and colleagues report the results of a trans-ancestry association study of inflammatory bowel disease. They implicate 38 new susceptibility loci, and show that the variance explained by each IBD risk locus is consistent across diverse ancestries, with a few notable exceptions. Ulcerative colitis and Crohn's disease are the two main forms of inflammatory bowel disease (IBD). Here we report the first trans-ancestry association study of IBD, with genome-wide or Immunochip genotype data from an extended cohort of 86,640 European individuals and Immunochip data from 9,846 individuals of East Asian, Indian or Iranian descent. We implicate 38 loci in IBD risk for the first time. For the majority of the IBD risk loci, the direction and magnitude of effect are consistent in European and non-European cohorts. Nevertheless, we observe genetic heterogeneity between divergent populations at several established risk loci driven by differences in allele frequency (NOD2) or effect size (TNFSF15 and ATG16L1) or a combination of these factors (IL23R and IRGM). Our results provide biological insights into the pathogenesis of IBD and demonstrate the usefulness of trans-ancestry association studies for mapping loci associated with complex diseases and understanding genetic architecture across diverse populations.
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In humans, polymorphisms in several autophagy-related genes (IRGM, LRRK2, SMURF1, ATG16L1) leading to autophagy deficiency are linked to IBD susceptibility.
“In humans, polymorphisms in several autophagy-related genes, including IRGM, LRRK2, SMURF1 and ATG16L1, leading to autophagy deficiency are linked to inflammatory bowel disease (IBD) susceptibility50.”
From Selective degradation of PU.1 during autophagy represses the differentiation and antitumour activity of TH9 cells (2017) · cites this paper as [50]
The Results section, “Biological implications of newly associated IBD loci” (page unavailable), identifies ATG16L1 and IRGM as Crohn’s disease susceptibility genes and links autophagy to its pathogenesis. The cited passages do not establish the claimed links for LRRK2 or SMURF1, or show that the associated variants cause autophagy deficiency. (LLM, conf=0.88)
Experimental — accuracy not yet measuredLD differences drive differences in effect size estimates from GWAS across populations in proportion to LD between tagging and causal SNP pairs, even when causal effects are the same.
“These LD differences in turn drive differences in effect size estimates (i.e. predictors) from GWAS across populations in proportion to LD between tagging and causal SNP pairs, even when causal effects are the same35,37–40 (Supplementary Note).”
From Clinical use of current polygenic risk scores may exacerbate health disparities (2019) · cites this paper as [35]
Online Methods (Trans-ethnic association analysis; page not provided) says differences in LD between populations can produce differences in allelic effect estimates, and the Discussion says differential tagging of untyped causal variants could explain observed effect-size heterogeneity. The paper does not establish that the differences are proportional to LD between tagging and causal SNPs, or show this occurring when causal effects are the same; it presents differential tagging as a possibility rather than the demonstrated cause. (LLM, conf=0.86)
Experimental — accuracy not yet measuredLinkage disequilibrium differentiates marginal effect size estimates for polygenic traits across populations, even when causal variants are the same.
“2) linkage disequilibrium (LD) differentiates marginal effect size estimates for polygenic traits across populations, even when causal variants are the same;”
From Clinical use of current polygenic risk scores may exacerbate health disparities (2019) · cites this paper as [35]
The Online Methods (Trans-ethnic association analysis; page unavailable) say that differences in LD with a causal variant can produce differences in observed allelic effects across populations. The Discussion (page unavailable) likewise identifies differential tagging of untyped causal variants as a possible explanation for effect-size heterogeneity. The paper does not establish that LD does so generally for polygenic traits; it presents the mechanism as a possibility in its IBD analysis. (LLM, conf=0.84)
Experimental — accuracy not yet measuredCommon factors in the pathophysiology of Crohn's and Parkinson's diseases include variants in the CARD15 and LRRK2 genes involved in the pathogenesis of both diseases.
“There are common factors in the pathophysiology of Crohn's and Parkinson's diseases, e.g., variants in the CARD15 and LRRK2 genes are involved in the pathogenesis of both diseases [393][394][395].”
From The Role of Microbiota-Gut-Brain Axis in Neuropsychiatric and Neurological Disorders (2021) · cites this paper as [395]
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- Authors
- Liu, J. Z., van Sommeren, S., Huang, H., Ng, S. C., Alberts, R., Takahashi, A., Ripke, S., Lee, J. C., Jostins, L., Shah, T., Abedian, S., Cheon, J. H., Cho, J., Daryani, N. E., Franke, L., Fuyuno, Y., Hart, A., Juyal, R. C., Juyal, G., Kim, W. H., Morris, A. P., Poustchi, H., Newman, W. G., Midha, V., Orchard, T. R., Vahedi, H., Sood, A., Sung, J. J. Y., Malekzadeh, R., Westra, H.-J., Yamazaki, K., Yang, S.-K., International Multiple Sclerosis Genetics Consortium, International IBD Genetics Consortium, Barrett, J. C., Franke, A., Alizadeh, B. Z., Parkes, M., B K, T., Daly, M. J., Kubo, M., Anderson, C. A., & Weersma, R. K.
- Affiliations
- Wellcome Sanger Institute (GB)
- Harvard University (US)
- Chinese University of Hong Kong (HK)
- University Medical Center Groningen (NL)
- RIKEN Center for Integrative Medical Sciences (JP)
- Addenbrooke's Hospital (GB)
- Shariati Hospital (IR)
- Yonsei University (KR)
- Mount Sinai Hospital (US)
- RIKEN (JP)
- St Mark's Hospital (GB)
- National Institute of Immunology (IN)
- University of Delhi (IN)
- Centre for Human Genetics (GB)
- National Health Service (GB)
- Dayanand Medical College & Hospital (IN)
- St Mary's Hospital (GB)
- Asan Medical Center (KR)
- Christian-Albrechts-Universität zu Kiel (DE)
- Corresponding author
- Anderson, Carl A
- Weersma, Rinse K
- ORCID
- Liu, Jimmy Z
- Huang, Hailiang
- Ng, Siew C
- Alberts, Rudi
- Takahashi, Atsushi
- Ripke, Stephan
- Lee, James C
- Cheon, Jae Hee
- Cho, Judy
- Franke, Lude
- Fuyuno, Yuta
- Juyal, Garima
- Kim, Won Ho
- Morris, Andrew P
- Poustchi, Hossein
- Newman, William G
- Midha, Vandana
- Orchard, Timothy R
- Sood, Ajit
- Sung, Joseph J Y
- Malekzadeh, Reza
- Westra, Harm-Jan
- Yang, Suk-Kyun
- Barrett, Jeffrey C
- Franke, Andre
- Alizadeh, Behrooz Z
- Parkes, Miles
- Daly, Mark J
- Kubo, Michiaki
- Anderson, Carl A
- Weersma, Rinse K
- Venue
- Nature Genetics
- Published
- 2015-07-20
- Volume
- 47
- Issue
- 9
- Pages
- 979-986
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC4881818
- OpenAlex
- W1014257459
- Cited by
- 2,603
- References
- 55
- Citations by year
- 2026: 153 · 2025: 230 · 2024: 342 · 2023: 296 · 2022: 265 · 2021: 246 · 2020: 255 · 2019: 272 · 2018: 211 · 2017: 196 · 2016: 118 · 2015: 15 · 2014: 1
- FWCI
- 123.00
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature Genetics (publishedVersion, other-oa)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- UWA Profiles and Research Repository (UWA) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Ghent University Academic Bibliography (Ghent University) (submittedVersion)
- Digital Access to Libraries (submittedVersion, other-oa)
- Discovery Research Portal (University of Dundee) (submittedVersion)
- Florence Research (University of Florence) (submittedVersion)
- Repository@Nottingham (University of Nottingham) (submittedVersion, cc-by)
- YUHSpace (Yonsei University Medical Library) (submittedVersion, cc-by-nc-nd)
- IRIS Research product catalog (Sapienza University of Rome) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- Lithuanian University of Health Sciences (submittedVersion)
- Repository@Nottingham (University of Nottingham) (submittedVersion)
- Open Repository and Bibliography (University of Liège) (submittedVersion, other-oa)
- Research Explorer (The University of Manchester) (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
- University of Southern Denmark Research Portal (University of Southern Denmark) (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion)
- Funders
- Eli and Edythe Broad Foundation
- Wellcome Trust (FP7/2007–2013, 098017, 102974/Z/13/Z, WT098017, 102974, 098051)
- Crohn's and Colitis Foundation (IBD-0318R-2)
- National Institute for Health and Care Research (FP7/2007–2013, NIHR-RP-R3-12-026, CL-2014-01-005)
- King's College London
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (FP7 2007-2013, 916·10·135, 917.14.374, 016.136.308)
- Crohn's and Colitis UK (M11-2, M11-1)
- Tehran University of Medical Sciences and Health Services
- Medical Research Council (FP7/20072013, 259867, 098051)
- Japan Society for the Promotion of Science (26293180)
- National Institute of Diabetes and Digestive and Kidney Diseases (U01DK062420, U01DK062429, P30DK043351, U01DK062423)
- National Institute of Neurological Disorders and Stroke (R01NS049477)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Inflammatory Bowel Disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Health Sciences › Medicine › Ophthalmology › Ocular Diseases and Behçet’s Syndrome
- Keywords
- inflammatory bowel disease, ulcerative colitis, Crohn's disease, genetic susceptibility loci, genetic heterogeneity, NOD2, TNFSF15, ATG16L1, IL23R, IRGM, allele frequency differences, effect size heterogeneity, genetic architecture, East Asian populations, non-European populations
- MeSH terms
- Colitis, Ulcerative, Crohn Disease, Gene Frequency, Humans, Risk Factors, Case-Control Studies, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Genetic Loci
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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