Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease
Open accessAbstract
More than 1,000 susceptibility loci have been identified through genome-wide association studies (GWAS) of common variants; however, the specific genes and full allelic spectrum of causal variants underlying these findings have not yet been defined. Here we used pooled next-generation sequencing to study 56 genes from regions associated with Crohn's disease in 350 cases and 350 controls. Through follow-up genotyping of 70 rare and low-frequency protein-altering variants in nine independent case-control series (16,054 Crohn's disease cases, 12,153 ulcerative colitis cases and 17,575 healthy controls), we identified four additional independent risk factors in NOD2, two additional protective variants in IL23R, a highly significant association with a protective splice variant in CARD9 (P < 1 × 10(-16), odds ratio ≈ 0.29) and additional associations with coding variants in IL18RAP, CUL2, C1orf106, PTPN22 and MUC19. We extend the results of successful GWAS by identifying new, rare and probably functional variants that could aid functional experiments and predictive models.
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This enables more rigorous evaluation of the contribution of rare and common variants to trait susceptibility and supports enumeration of allelic series critical for studies of disease mechanism and therapeutic target optimization.
“This enables more rigorous evaluation of the contribution of rare and common variants to trait susceptibility48 and supports the enumeration of ‘allelic series’ (sets of alleles of varying frequency, effect size and direction that disrupt the same gene) critical for studies of disease mechanism and therapeutic target optimization89,96.”
From A brief history of human disease genetics (2020) · cites this paper as [96]
An initial inflammatory bowel disease screen found rare-variant evidence for just one of 63 GWAS-identified genes.
“only 1 of 63 genes in an initial screen for inflammatory bowel disease found evidence for rare variant effects (and these were protective114, but see also115)”
From Rare and common variants: twenty arguments (2012) · cites this paper as [115]
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- Authors
- National Institute of Diabetes and Digestive Kidney Diseases Inflammatory Bowel Disease Genetics Consortium (NIDDK IBDGC), Rivas, M. A., United Kingdom Inflammatory Bowel Disease Genetics Consortium, International Inflammatory Bowel Disease Genetics Consortium, Beaudoin, M., Gardet, A., Stevens, C., Sharma, Y., Zhang, C. K., Boucher, G., Ripke, S., Ellinghaus, D., Burtt, N., Fennell, T., Kirby, A., Latiano, A., Goyette, P., Green, T., Halfvarson, J., Haritunians, T., Korn, J. M., Kuruvilla, F., Lagacé, C., Neale, B., Lo, K. S., Schumm, P., Törkvist, L., Dubinsky, M. C., Brant, S. R., Silverberg, M. S., Duerr, R. H., Altshuler, D., Gabriel, S., Lettre, G., Franke, A., D'Amato, M., McGovern, D. P. B., Cho, J. H., Rioux, J. D., Xavier, R. J., & Daly, M. J.
- Affiliations
- Broad Institute (US)
- Montreal Heart Institute (CA)
- Yale University (US)
- Christian-Albrechts-Universität zu Kiel (DE)
- Casa Sollievo della Sofferenza (IT)
- Örebro University (SE)
- Cedars-Sinai Medical Center (US)
- Karolinska Institutet (SE)
- Johns Hopkins University (US)
- Mount Sinai Hospital (CA)
- University of Pittsburgh (US)
- Corresponding author
- Rivas, Manuel A
- Daly, Mark J
- ORCID
- Rivas, Manuel A
- Beaudoin, Mélissa
- Stevens, Christine
- Sharma, Yashoda
- Boucher, Gabrielle
- Ripke, Stephan
- Ellinghaus, David
- Fennell, Tim
- Latiano, Anna
- Halfvarson, Jonas
- Haritunians, Talin
- Korn, Joshua M
- Neale, Benjamin
- Lo, Ken Sin
- Dubinsky, Marla C
- Brant, Steven R
- Silverberg, Mark S
- Duerr, Richard H
- Altshuler, David
- Gabriel, Stacey
- Lettre, Guillaume
- McGovern, Dermot P B
- Cho, Judy H
- Rioux, John D
- Xavier, Ramnik J
- Daly, Mark J
- Venue
- Nature Genetics
- Published
- 2011-10-09
- Volume
- 43
- Issue
- 11
- Pages
- 1066-1073
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC3378381
- OpenAlex
- W2097804771
- Cited by
- 771
- References
- 47
- Citations by year
- 2026: 17 · 2025: 25 · 2024: 28 · 2023: 35 · 2022: 33 · 2021: 47 · 2020: 35 · 2019: 60 · 2018: 49 · 2017: 42 · 2016: 64 · 2015: 75 · 2014: 83 · 2013: 95 · 2012: 77
- FWCI
- 52.08
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Discovery Research Portal (University of Dundee) (publishedVersion)
- Pure Amsterdam UMC (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Rutgers University Community Repository (Rutgers University) (submittedVersion)
- UWA Profiles and Research Repository (UWA) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- Ghent University Academic Bibliography (Ghent University) (submittedVersion)
- Bern Open Repository and Information System (University of Bern) (submittedVersion)
- Open Repository and Bibliography (University of Liège) (submittedVersion, other-oa)
- RWTH Publications (RWTH Aachen) (submittedVersion)
- Radboud Repository (Radboud University) (submittedVersion)
- Funders
- Crohn's and Colitis Foundation of America (DK062422)
- Leona M. and Harry B. Helmsley Charitable Trust
- Crohn's and Colitis Foundation
- Cedars-Sinai Medical Center
- Broad Institute
- Crohn's and Colitis Foundation of Canada
- Deutsche Forschungsgemeinschaft
- Örebro Universitet
- Crohn's and Colitis UK (M11-1)
- Vetenskapsrådet
- Universitetssjukhuset Örebro
- Exzellenzclusters Entzündungsforschung
- Institut de Cardiologie de Montréal
- National Institutes of Health (M01-RR00425, DK062429, RR00425, DK-063491, DK 043351, DK062413, DK046763)
- Canadian Institutes of Health Research (01038)
- National Human Genome Research Institute (U54HG003067, U01HG005923, HG005923)
- National Institute of Allergy and Infectious Diseases (P01AI065687, U19AI067152, AI065687, AI-067152, AI 062773, R01AI062773)
- National Institute of Diabetes and Digestive and Kidney Diseases (DK063491, DK-06-2423, (DK043351, R01DK083756, P01DK046763, DK062429, DK062413, DK062420, R21DK084554, DK064869, DK086502, RC1DK086502, DK060049, DK 83756, DK062431, DK062422, DK062432, R21-DK84554-01, DK046763, R01DK064869, U01DK062420, M01-RR00425, U01DK062429, R01DK060049, U24DK062429, U01DK062413, U01DK062422, P30DK063491, U01DK062432, P30DK043351, U01DK062431, U01DK062423)
- National Center for Research Resources (M01RR000425, M01-RR00425)
- 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, Crohn's disease, ulcerative colitis, rare variants, NOD2, IL23R, IL18RAP, CUL2, PTPN22, MUC19, genetic susceptibility loci, protein-altering variants
- MeSH terms
- Cell Line, Humans, RNA Splicing, Inflammatory Bowel Diseases, Case-Control Studies, Sequence Analysis, DNA, Receptors, Interleukin, Genetic Predisposition to Disease, Nod2 Signaling Adaptor Protein, Genome-Wide Association Study
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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.
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