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Hov JR, Keitel V, Laerdahl JK, Spomer L, Ellinghaus E, ElSharawy A, Melum E, Boberg KM, Manke T, Balschun T, Schramm C, Bergquist A, Weismüller T, Gotthardt D, Rust C, Henckaerts L, Onnie CM, Weersma RK, Sterneck M, Teufel A, Runz H, Stiehl A, Ponsioen CY, Wijmenga C, Vatn MH, Stokkers PCF, Vermeire S, Mathew CG, Lie BA, Beuers U, Manns MP, Schreiber S, Schrumpf E, Häussinger D, Franke A, Karlsen TH. Mutational characterization of the bile acid receptor TGR5 in primary sclerosing cholangitis. PLoS One 2010; 5:e12403. [PMID: 20811628 PMCID: PMC2928275 DOI: 10.1371/journal.pone.0012403] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Accepted: 07/14/2010] [Indexed: 12/14/2022] Open
Abstract
Background TGR5, the G protein-coupled bile acid receptor 1 (GPBAR1), has been linked to inflammatory pathways as well as bile homeostasis, and could therefore be involved in primary sclerosing cholangitis (PSC) a chronic inflammatory bile duct disease. We aimed to extensively investigate TGR5 sequence variation in PSC, as well as functionally characterize detected variants. Methodology/Principal Findings Complete resequencing of TGR5 was performed in 267 PSC patients and 274 healthy controls. Six nonsynonymous mutations were identified in addition to 16 other novel single-nucleotide polymorphisms. To investigate the impact from the nonsynonymous variants on TGR5, we created a receptor model, and introduced mutated TGR5 constructs into human epithelial cell lines. By using confocal microscopy, flow cytometry and a cAMP-sensitive luciferase assay, five of the nonsynonymous mutations (W83R, V178M, A217P, S272G and Q296X) were found to reduce or abolish TGR5 function. Fine-mapping of the previously reported PSC and UC associated locus at chromosome 2q35 in large patient panels revealed an overall association between the TGR5 single-nucleotide polymorphism rs11554825 and PSC (odds ratio = 1.14, 95% confidence interval: 1.03–1.26, p = 0.010) and UC (odds ratio = 1.19, 95% confidence interval 1.11–1.27, p = 8.5×10−7), but strong linkage disequilibrium precluded demarcation of TGR5 from neighboring genes. Conclusions/Significance Resequencing of TGR5 along with functional investigations of novel variants provided unique insight into an important candidate gene for several inflammatory and metabolic conditions. While significant TGR5 associations were detected in both UC and PSC, further studies are needed to conclusively define the role of TGR5 variation in these diseases.
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MESH Headings
- Adolescent
- Adult
- Aged
- Amino Acid Sequence
- Animals
- Cattle
- Child
- Cholangitis, Sclerosing/complications
- Cholangitis, Sclerosing/genetics
- Cholangitis, Sclerosing/metabolism
- Chromosomes, Human, Pair 2/genetics
- Colitis, Ulcerative/complications
- DNA Mutational Analysis
- Dogs
- Female
- Gene Expression Regulation
- Humans
- Male
- Mice
- Middle Aged
- Models, Molecular
- Mutation
- Protein Conformation
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/genetics
- Receptors, G-Protein-Coupled/metabolism
- Young Adult
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Affiliation(s)
- Johannes R Hov
- Norwegian PSC Research Center, Clinic for Specialized Medicine and Surgery, Oslo University Hospital Rikshospitalet, Oslo, Norway.
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2
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Prescott NJ, Dominy KM, Kubo M, Lewis CM, Fisher SA, Redon R, Huang N, Stranger BE, Blaszczyk K, Hudspith B, Parkes G, Hosono N, Yamazaki K, Onnie CM, Forbes A, Dermitzakis ET, Nakamura Y, Mansfield JC, Sanderson J, Hurles ME, Roberts RG, Mathew CG. Independent and population-specific association of risk variants at the IRGM locus with Crohn's disease. Hum Mol Genet 2010; 19:1828-39. [PMID: 20106866 PMCID: PMC2850616 DOI: 10.1093/hmg/ddq041] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
DNA polymorphisms in a region on chromosome 5q33.1 which contains two genes, immunity related GTPase related family, M (IRGM) and zinc finger protein 300 (ZNF300), are associated with Crohn's disease (CD). The deleted allele of a 20 kb copy number variation (CNV) upstream of IRGM was recently shown to be in strong linkage disequilibrium (LD) with the CD-associated single nucleotide polymorphisms and is itself associated with CD (P < 0.01). The deletion was correlated with increased or reduced expression of IRGM in transformed cells in a cell line-dependent manner, and has been proposed as a likely causal variant. We report here that small insertion/deletion polymorphisms in the promoter and 5' untranslated region of IRGM are, together with the CNV, strongly associated with CD (P = 1.37 x 10(-5) to 1.40 x 10(-9)), and that the CNV and the 5'-untranslated region variant -308(GTTT)(5) contribute independently to CD susceptibility (P = 2.6 x 10(-7) and P = 2 x 10(-5), respectively). We also show that the CD risk haplotype is associated with a significant decrease in IRGM expression (P < 10(-12)) in untransformed lymphocytes from CD patients. Further analysis of these variants in a Japanese CD case-control sample and of IRGM expression in HapMap populations revealed that neither the IRGM insertion/deletion polymorphisms nor the CNV was associated with CD or with altered IRGM expression in the Asian population. This suggests that the involvement of the IRGM risk haplotype in the pathogenesis of CD requires gene-gene or gene-environment interactions which are absent in Asian populations, or that none of the variants analysed are causal, and that the true causal variants arose after the European-Asian split.
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Affiliation(s)
- Natalie J Prescott
- Department of Medical and Molecular Genetics, King's College London School of Medicine, Guy's Hospital, London SE1 9RT, UK.
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3
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Imielinski M, Baldassano RN, Griffiths A, Russell RK, Annese V, Dubinsky M, Kugathasan S, Bradfield JP, Walters TD, Sleiman P, Kim CE, Muise A, Wang K, Glessner JT, Saeed S, Zhang H, Frackelton EC, Hou C, Flory JH, Otieno G, Chiavacci RM, Grundmeier R, Castro M, Latiano A, Dallapiccola B, Stempak J, Abrams DJ, Taylor K, McGovern D, Silber G, Wrobel I, Quiros A, Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmuda MM, Bitton A, Dassopoulos T, Datta LW, Green T, Griffiths AM, Kistner EO, Murtha MT, Regueiro MD, Rotter JI, Schumm LP, Steinhart AH, Targan SR, Xavier RJ, Libioulle C, Sandor C, Lathrop M, Belaiche J, Dewit O, Gut I, Heath S, Laukens D, Mni M, Rutgeerts P, Van Gossum A, Zelenika D, Franchimont D, Hugot JP, de Vos M, Vermeire S, Louis E, Cardon LR, Anderson CA, Drummond H, Nimmo E, Ahmad T, Prescott NJ, Onnie CM, Fisher SA, Marchini J, Ghori J, Bumpstead S, Gwillam R, Tremelling M, Delukas P, Mansfield J, Jewell D, Satsangi J, Mathew CG, Parkes M, Georges M, Daly MJ, Heyman MB, Ferry GD, Kirschner B, Lee J, Essers J, Grand R, Stephens M, Levine A, Piccoli D, Van Limbergen J, Cucchiara S, Monos DS, Guthery SL, Denson L, Wilson DC, Grant SFA, Daly M, Silverberg MS, Satsangi J, Hakonarson H. Common variants at five new loci associated with early-onset inflammatory bowel disease. Nat Genet 2009; 41:1335-40. [PMID: 19915574 DOI: 10.1038/ng.489] [Citation(s) in RCA: 379] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 10/22/2009] [Indexed: 12/13/2022]
Abstract
The inflammatory bowel diseases (IBD) Crohn's disease and ulcerative colitis are common causes of morbidity in children and young adults in the western world. Here we report the results of a genome-wide association study in early-onset IBD involving 3,426 affected individuals and 11,963 genetically matched controls recruited through international collaborations in Europe and North America, thereby extending the results from a previous study of 1,011 individuals with early-onset IBD. We have identified five new regions associated with early-onset IBD susceptibility, including 16p11 near the cytokine gene IL27 (rs8049439, P = 2.41 x 10(-9)), 22q12 (rs2412973, P = 1.55 x 10(-9)), 10q22 (rs1250550, P = 5.63 x 10(-9)), 2q37 (rs4676410, P = 3.64 x 10(-8)) and 19q13.11 (rs10500264, P = 4.26 x 10(-10)). Our scan also detected associations at 23 of 32 loci previously implicated in adult-onset Crohn's disease and at 8 of 17 loci implicated in adult-onset ulcerative colitis, highlighting the close pathogenetic relationship between early- and adult-onset IBD.
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Affiliation(s)
- Marcin Imielinski
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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4
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Chapman JM, Onnie CM, Prescott NJ, Fisher SA, Mansfield JC, Mathew CG, Lewis CM, Verzilli CJ, Whittaker JC. Searching for genotype-phenotype structure: using hierarchical log-linear models in Crohn disease. Am J Hum Genet 2009; 84:178-87. [PMID: 19185283 DOI: 10.1016/j.ajhg.2008.12.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 12/02/2008] [Accepted: 12/29/2008] [Indexed: 02/03/2023] Open
Abstract
There has been considerable recent success in the detection of gene-disease associations. We consider here the development of tools that facilitate the more detailed characterization of the effect of a genetic variant on disease. We replace the simplistic classification of individuals according to a single binary disease indicator with classification according to a number of subphenotypes. This more accurately reflects the underlying biological complexity of the disease process, but it poses additional analytical difficulties. Notably, the subphenotypes that make up a particular disease are typically highly associated, and it becomes difficult to distinguish which genes might be causing which subphenotypes. Such problems arise in many complex diseases. Here, we concentrate on an application to Crohn disease (CD). We consider this problem as one of model selection based upon log-linear models, fitted in a Bayesian framework via reversible-jump Metropolis-Hastings approach. We evaluate the performance of our suggested approach with a simple simulation study and then apply the method to a real data example in CD, revealing a sparse disease structure. Most notably, the associated NOD2.908G-->R mutation appears to be directly related to more severe disease behaviors, whereas the other two associated NOD2 variants, 1007L-->FS and 702R-->W, are more generally related to disease in the small bowel (ileum and jejenum). The ATG16L1.300T-->A variant appears to be directly associated with only disease of the small bowel.
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Affiliation(s)
- Juliet M Chapman
- Department of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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5
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Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmada MM, Bitton A, Dassopoulos T, Datta LW, Green T, Griffiths AM, Kistner EO, Murtha MT, Regueiro MD, Rotter JI, Schumm LP, Steinhart AH, Targan SR, Xavier RJ, Libioulle C, Sandor C, Lathrop M, Belaiche J, Dewit O, Gut I, Heath S, Laukens D, Mni M, Rutgeerts P, Van Gossum A, Zelenika D, Franchimont D, Hugot JP, de Vos M, Vermeire S, Louis E, Cardon LR, Anderson CA, Drummond H, Nimmo E, Ahmad T, Prescott NJ, Onnie CM, Fisher SA, Marchini J, Ghori J, Bumpstead S, Gwilliam R, Tremelling M, Deloukas P, Mansfield J, Jewell D, Satsangi J, Mathew CG, Parkes M, Georges M, Daly MJ. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet 2008; 40:955-62. [PMID: 18587394 PMCID: PMC2574810 DOI: 10.1038/ng.175] [Citation(s) in RCA: 1991] [Impact Index Per Article: 124.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Accepted: 05/02/2008] [Indexed: 02/07/2023]
Abstract
Several risk factors for Crohn's disease have been identified in recent genome-wide association studies. To advance gene discovery further, we combined data from three studies on Crohn's disease (a total of 3,230 cases and 4,829 controls) and carried out replication in 3,664 independent cases with a mixture of population-based and family-based controls. The results strongly confirm 11 previously reported loci and provide genome-wide significant evidence for 21 additional loci, including the regions containing STAT3, JAK2, ICOSLG, CDKAL1 and ITLN1. The expanded molecular understanding of the basis of this disease offers promise for informed therapeutic development.
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Affiliation(s)
- Jeffrey C Barrett
- Bioinformatics and Statistical Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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6
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Fisher SA, Tremelling M, Anderson CA, Gwilliam R, Bumpstead S, Prescott NJ, Nimmo ER, Massey D, Berzuini C, Johnson C, Barrett JC, Cummings FR, Drummond H, Lees CW, Onnie CM, Hanson CE, Blaszczyk K, Inouye M, Ewels P, Ravindrarajah R, Keniry A, Hunt S, Carter M, Watkins N, Ouwehand W, Lewis CM, Cardon L, Lobo A, Forbes A, Sanderson J, Jewell DP, Mansfield JC, Deloukas P, Mathew CG, Parkes M, Satsangi J. Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease. Nat Genet 2008; 40:710-2. [PMID: 18438406 PMCID: PMC2719289 DOI: 10.1038/ng.145] [Citation(s) in RCA: 333] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Accepted: 03/14/2008] [Indexed: 12/11/2022]
Abstract
We report results of a nonsynonymous SNP scan for ulcerative colitis and identify a previously unknown susceptibility locus at ECM1. We also show that several risk loci are common to ulcerative colitis and Crohn's disease (IL23R, IL12B, HLA, NKX2-3 and MST1), whereas autophagy genes ATG16L1 and IRGM, along with NOD2 (also known as CARD15), are specific for Crohn's disease. These data provide the first detailed illustration of the genetic relationship between these common inflammatory bowel diseases.
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Affiliation(s)
- Sheila A Fisher
- Department of Medical and Molecular Genetics, King's College London School of Medicine, 8th Floor Guy's Tower, Guy's Hospital, London SE1 9RT, UK
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7
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Franke A, Hampe J, Rosenstiel P, Becker C, Wagner F, Häsler R, Little RD, Huse K, Ruether A, Balschun T, Wittig M, ElSharawy A, Mayr G, Albrecht M, Prescott NJ, Onnie CM, Fournier H, Keith T, Radelof U, Platzer M, Mathew CG, Stoll M, Krawczak M, Nürnberg P, Schreiber S. Systematic association mapping identifies NELL1 as a novel IBD disease gene. PLoS One 2007; 2:e691. [PMID: 17684544 PMCID: PMC1933598 DOI: 10.1371/journal.pone.0000691] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Accepted: 06/20/2007] [Indexed: 12/14/2022] Open
Abstract
Crohn disease (CD), a sub-entity of inflammatory bowel disease (IBD), is a complex polygenic disorder. Although recent studies have successfully identified CD-associated genetic variants, these susceptibility loci explain only a fraction of the heritability of the disease. Here, we report on a multi-stage genome-wide scan of 393 German CD cases and 399 controls. Among the 116,161 single-nucleotide polymorphisms tested, an association with the known CD susceptibility gene NOD2, the 5q31 haplotype, and the recently reported CD locus at 5p13.1 was confirmed. In addition, SNP rs1793004 in the gene encoding nel-like 1 precursor (NELL1, chromosome 11p15.1) showed a consistent disease-association in independent German population- and family-based samples (942 cases, 1082 controls, 375 trios). Subsequent fine mapping and replication in an independent sample of 454 French/Canadian CD trios supported the authenticity of the NELL1 association. Further confirmation in a large German ulcerative colitis (UC) sample indicated that NELL1 is a ubiquitous IBD susceptibility locus (combined p<10−6; OR = 1.66, 95% CI: 1.30–2.11). The novel 5p13.1 locus was also replicated in the French/Canadian sample and in an independent UK CD patient panel (453 cases, 521 controls, combined p<10−6 for SNP rs1992660). Several associations were replicated in at least one independent sample, point to an involvement of ITGB6 (upstream), GRM8 (downstream), OR5V1 (downstream), PPP3R2 (downstream), NM_152575 (upstream) and HNF4G (intron).
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Affiliation(s)
- Andre Franke
- Institute for Clinical Molecular Biology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Jochen Hampe
- First Department of Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Philip Rosenstiel
- Institute for Clinical Molecular Biology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Christian Becker
- Cologne Center for Genomics, University of Cologne, Köln, Germany
- RZPD German Resource Center for Genome Research, Berlin, Germany
| | - Florian Wagner
- RZPD German Resource Center for Genome Research, Berlin, Germany
| | - Robert Häsler
- Institute for Clinical Molecular Biology, Christian-Albrechts University Kiel, Kiel, Germany
| | | | - Klaus Huse
- Genome Analysis Group, Leibniz Institute for Age Research, Jena, Germany
| | - Andreas Ruether
- PopGen Biobank, Christian-Albrechts University Kiel, Kiel, Germany
| | - Tobias Balschun
- Institute for Clinical Molecular Biology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Michael Wittig
- PopGen Biobank, Christian-Albrechts University Kiel, Kiel, Germany
| | - Abdou ElSharawy
- Institute for Clinical Molecular Biology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Gabriele Mayr
- Max-Planck Institute for Informatics, Saarbrücken, Germany
| | - Mario Albrecht
- Max-Planck Institute for Informatics, Saarbrücken, Germany
| | - Natalie J. Prescott
- Department of Medical and Molecular Genetics, King's College London School of Medicine, London, United Kingdom
| | - Clive M. Onnie
- Department of Medical and Molecular Genetics, King's College London School of Medicine, London, United Kingdom
| | | | - Tim Keith
- Genizon BioSciences5, Québec, Canada
| | - Uwe Radelof
- RZPD German Resource Center for Genome Research, Berlin, Germany
| | - Matthias Platzer
- Genome Analysis Group, Leibniz Institute for Age Research, Jena, Germany
| | - Christopher G. Mathew
- Department of Medical and Molecular Genetics, King's College London School of Medicine, London, United Kingdom
| | - Monika Stoll
- Leibniz-Institute for Arteriosclerosis Research, University Münster, Münster, Germany
| | - Michael Krawczak
- PopGen Biobank, Christian-Albrechts University Kiel, Kiel, Germany
- Institute of Medical Statistics and Informatics, Christian-Albrechts University Kiel, Kiel, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Köln, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Köln, Germany
| | - Stefan Schreiber
- Institute for Clinical Molecular Biology, Christian-Albrechts University Kiel, Kiel, Germany
- First Department of Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
- PopGen Biobank, Christian-Albrechts University Kiel, Kiel, Germany
- * To whom correspondence should be addressed. E-mail:
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Parkes M, Barrett JC, Prescott NJ, Tremelling M, Anderson CA, Fisher SA, Roberts RG, Nimmo ER, Cummings FR, Soars D, Drummond H, Lees CW, Khawaja SA, Bagnall R, Burke DA, Todhunter CE, Ahmad T, Onnie CM, McArdle W, Strachan D, Bethel G, Bryan C, Lewis CM, Deloukas P, Forbes A, Sanderson J, Jewell DP, Satsangi J, Mansfield JC, Cardon L, Mathew CG. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat Genet 2007; 39:830-2. [PMID: 17554261 PMCID: PMC2628541 DOI: 10.1038/ng2061] [Citation(s) in RCA: 867] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Accepted: 05/11/2007] [Indexed: 02/06/2023]
Abstract
A genome-wide association scan in individuals with Crohn's disease by the Wellcome Trust Case Control Consortium detected strong association at four novel loci. We tested 37 SNPs from these and other loci for association in an independent case-control sample. We obtained replication for the autophagy-inducing IRGM gene on chromosome 5q33.1 (replication P = 6.6 x 10(-4), combined P = 2.1 x 10(-10)) and for nine other loci, including NKX2-3, PTPN2 and gene deserts on chromosomes 1q and 5p13.
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Affiliation(s)
- Miles Parkes
- Inflammatory Bowel Disease Research Group, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 2QQ, UK.
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9
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Prescott NJ, Fisher SA, Franke A, Hampe J, Onnie CM, Soars D, Bagnall R, Mirza MM, Sanderson J, Forbes A, Mansfield JC, Lewis CM, Schreiber S, Mathew CG. A nonsynonymous SNP in ATG16L1 predisposes to ileal Crohn's disease and is independent of CARD15 and IBD5. Gastroenterology 2007; 132:1665-71. [PMID: 17484864 DOI: 10.1053/j.gastro.2007.03.034] [Citation(s) in RCA: 239] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Accepted: 03/18/2007] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS A genome-wide association scan of nonsynonymous DNA polymorphisms identified association of a threonine-to-alanine substitution (T300A) in the autophagy-related 16-like gene ATG16L1 with Crohn's disease. We investigated this association in independent U.K. cohorts of Crohn's disease and ulcerative colitis. METHODS The T300A variant (rs2241880) was genotyped in an independent sample of 727 Crohn's disease and 877 ulcerative colitis cases, and in 579 controls. We then performed an extension analysis combining these data with the U.K. data from the initial study to give a total of 1236 U.K. Crohn's disease cases and 1235 controls to estimate disease risk and test for interaction with the CARD15 and IBD5 risk loci and for association with disease subtypes. RESULTS The association of T300A was replicated in the independent sample of 727 Crohn's disease cases (P = .001), and was strongly associated in the extended analysis of 1236 Crohn's cases (P = 2.4 x 10(-6)). The 300A/A genotype conferred a 1.65-fold risk of Crohn's disease, with a 2.2-fold risk of ileal disease. Analysis of the interaction of ATG16L1 with CARD15 and IBD5 indicated that all 3 loci contribute independently to disease risk. Homozygosity for the risk allele at all 3 loci conferred a combined risk of 20.4 (95% confidence interval: 8.71, 47.7) for Crohn's disease. The ATG16L1 risk genotype showed a modest but significant association with ulcerative colitis (P = .026). CONCLUSIONS The association of ATG16L1 with Crohn's disease and possibly with ulcerative colitis supports a role for autophagy in the pathogenesis of inflammatory bowel disease.
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Affiliation(s)
- Natalie J Prescott
- Department of Medical and Molecular Genetics, King's College London School of Medicine, Guy's Hospital, London, UK
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10
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Tremelling M, Cummings F, Fisher SA, Mansfield J, Gwilliam R, Keniry A, Nimmo ER, Drummond H, Onnie CM, Prescott NJ, Sanderson J, Bredin F, Berzuini C, Forbes A, Lewis CM, Cardon L, Deloukas P, Jewell D, Mathew CG, Parkes M, Satsangi J. IL23R variation determines susceptibility but not disease phenotype in inflammatory bowel disease. Gastroenterology 2007; 132:1657-64. [PMID: 17484863 PMCID: PMC2696256 DOI: 10.1053/j.gastro.2007.02.051] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Accepted: 02/08/2007] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Identification of inflammatory bowel disease (IBD) susceptibility genes is key to understanding pathogenic mechanisms. Recently, the North American IBD Genetics Consortium provided compelling evidence for an association between ileal Crohn's disease (CD) and the IL23R gene using genome-wide association scanning. External replication is a priority, both to confirm this finding in other populations and to validate this new technique. We tested for association between IL23R and IBD in a large independent UK panel to determine the size of the effect and explore subphenotype correlation and interaction with CARD15. METHODS Eight single nucleotide polymorphism markers in IL23R tested in the North American study were genotyped in 1902 cases of Crohn's disease (CD), 975 cases of ulcerative colitis (UC), and 1345 controls using MassARRAY. Data were analyzed using chi(2) statistics, and subgroup association was sought. RESULTS A highly significant association with CD was observed, with the strongest signal at coding variant Arg381Gln (allele frequency, 2.5% in CD vs 6.2% in controls [P = 1.1 x 10(-12)]; odds ratio, 0.38; 95% confidence interval, 0.29-0.50). A weaker effect was seen in UC (allele frequency, 4.6%; odds ratio, 0.73; 95% confidence interval, 0.55-0.96). Analysis accounting for Arg381Gln suggested that other loci within IL23R also influence IBD susceptibility. Within CD, there were no subphenotype associations or evidence of interaction with CARD15. CONCLUSIONS This study shows an association between IL23R and all subphenotypes of CD with a smaller effect on UC. This extends the findings of the North American study, providing clear evidence that genome-wide association scanning can successfully identify true complex disease genes.
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Affiliation(s)
- Mark Tremelling
- IBD Research Group, Addenbrooke’s Hospital, University of Cambridge, Cambridge, England
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Fraser Cummings
- Gastroenterology Unit, Radcliffe Infirmary, University of Oxford, Oxford, England
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, England
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Sheila A. Fisher
- Division of Genetics and Molecular Medicine, Guy’s, King’s College and St Thomas’ School of Medicine, London, England
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - John Mansfield
- Faculty of Medical Sciences, University of Newcastle, Newcastle upon Tyne, England
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Rhian Gwilliam
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, England
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Andrew Keniry
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, England
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Elaine R. Nimmo
- Department of Gastroenterology, University of Edinburgh, and Gastrointestinal Unit, Western General Hospital, Edinburgh, Scotland
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Hazel Drummond
- Department of Gastroenterology, University of Edinburgh, and Gastrointestinal Unit, Western General Hospital, Edinburgh, Scotland
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Clive M. Onnie
- Department of Medical and Molecular Genetics, King’s College London School of Medicine, Guy’s Hospital, London, United Kingdom
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Natalie J. Prescott
- Department of Medical and Molecular Genetics, King’s College London School of Medicine, Guy’s Hospital, London, United Kingdom
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Jeremy Sanderson
- Division of Genetics and Molecular Medicine, Guy’s, King’s College and St Thomas’ School of Medicine, London, England
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Francesca Bredin
- IBD Research Group, Addenbrooke’s Hospital, University of Cambridge, Cambridge, England
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Carlo Berzuini
- IBD Research Group, Addenbrooke’s Hospital, University of Cambridge, Cambridge, England
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Alastair Forbes
- Department of Medical and Molecular Genetics, King’s College London School of Medicine, Guy’s Hospital, London, United Kingdom
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Cathryn M. Lewis
- Division of Genetics and Molecular Medicine, Guy’s, King’s College and St Thomas’ School of Medicine, London, England
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Lon Cardon
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, England
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, England
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Derek Jewell
- Gastroenterology Unit, Radcliffe Infirmary, University of Oxford, Oxford, England
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Christopher G. Mathew
- Division of Genetics and Molecular Medicine, Guy’s, King’s College and St Thomas’ School of Medicine, London, England
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Miles Parkes
- IBD Research Group, Addenbrooke’s Hospital, University of Cambridge, Cambridge, England
- Centre for Gastroenterology and Nutrition, University College, London, England
| | - Jack Satsangi
- Department of Gastroenterology, University of Edinburgh, and Gastrointestinal Unit, Western General Hospital, Edinburgh, Scotland
- Centre for Gastroenterology and Nutrition, University College, London, England
- Address requests for reprints to: Jack Satsangi, FRCP, Gastrointestinal Unit, Division of Medical Sciences, School of Molecular and Clinical Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, England. fax: (44) 0131-537-1085.
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Fisher SA, Mirza MM, Onnie CM, Soars D, Lewis CM, Prescott NJ, Mathew CG, Sanderson J, Forbes A, Todhunter C, Donaldson P, Mansfield J. Combined evidence from three large British Association studies rejects TUCAN/CARD8 as an IBD susceptibility gene. Gastroenterology 2007; 132:2078-80. [PMID: 17484911 DOI: 10.1053/j.gastro.2007.03.086] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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12
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Pearce AV, Fisher SA, Prescott NJ, Onnie CM, Pattni R, Green P, Forbes A, Mansfield J, Sanderson J, Schreiber S, Lewis CM, Mathew CG. Investigation of association of the DLG5 gene with phenotypes of inflammatory bowel disease in the British population. Int J Colorectal Dis 2007; 22:419-24. [PMID: 16944184 DOI: 10.1007/s00384-006-0151-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/02/2006] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND AIMS Mutations in the DLG5 gene are associated with an increased risk of inflammatory bowel disease (IBD) in some European populations. Initial investigation of a British IBD population showed evidence of association of one of three DLG5 variants, R30Q, in a family-based collection but not in a case-control cohort. We have now examined the association of the R30Q polymorphism in a large cohort of British IBD cases, tested for interaction between the DLG5 and CARD15 genes and assessed possible association of DLG5 with clinical features of Crohn's disease (CD) and ulcerative colitis (UC). MATERIALS AND METHODS DLG5 R30Q and the CARD15 polymorphisms, Arg702Trp, Gly908Arg and Leu1007fs were genotyped in 1,148 IBD cases and 749 controls. DLG5 R30Q was also analysed in cases stratified by CARD15 genotype, disease subtype and smoking history. RESULTS/FINDINGS No significant difference in frequencies of the R30Q variant was observed between IBD cases (9.9%) and controls (10.1%) or in cases analysed separately as CD and UC. There was also no significant difference in the frequency of R30Q between CD cases carrying risk-associated CARD15 alleles and those that did not. The frequency of R30Q was higher in CD cases with ileal disease than cases without (p=0.042) and higher in CD cases who had smoked than in nonsmokers (p=0.009). INTERPRETATION/CONCLUSION The R30Q variant in the DLG5 gene does not appear to be associated with an overall increase in the risk of disease in a British IBD cohort, but differences in its frequency in subgroups of CD patients warrant further investigation.
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Affiliation(s)
- Alexandra V Pearce
- Department of Medical & Molecular Genetics, King's College London School of Medicine, 8th Floor Guy's Tower, Guy's Hospital, London SE1 9RT, UK
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Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, Huse K, Albrecht M, Mayr G, De La Vega FM, Briggs J, Günther S, Prescott NJ, Onnie CM, Häsler R, Sipos B, Fölsch UR, Lengauer T, Platzer M, Mathew CG, Krawczak M, Schreiber S. A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet 2006; 39:207-11. [PMID: 17200669 DOI: 10.1038/ng1954] [Citation(s) in RCA: 1402] [Impact Index Per Article: 77.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Accepted: 12/05/2006] [Indexed: 11/08/2022]
Abstract
We performed a genome-wide association study of 19,779 nonsynonymous SNPs in 735 individuals with Crohn disease and 368 controls. A total of 7,159 of these SNPs were informative. We followed up on all 72 SNPs with P <or= 0.01 with an allele-based disease association test in 380 independent Crohn disease trios, 498 Crohn disease singleton cases and 1,032 controls. Disease association of rs2241880 in the autophagy-related 16-like 1 gene (ATG16L1) was replicated in these samples (P = 4.0 x 10(-8)) and confirmed in a UK case-control sample (P = 0.0004). By haplotype and regression analysis, we found that marker rs2241880, a coding SNP (T300A), carries virtually all the disease risk exerted by the ATG16L1 locus. The ATG16L1 gene encodes a protein in the autophagosome pathway that processes intracellular bacteria. We found a statistically significant interaction with respect to Crohn disease risk between rs2241880 and the established CARD15 susceptibility variants (P = 0.039). Together with the lack of association between rs2241880 and ulcerative colitis (P > 0.4), these data suggest that the underlying biological process may be specific to Crohn disease.
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Affiliation(s)
- Jochen Hampe
- Institute for Clinical Molecular Biology, Christian-Albrechts University Kiel, University Hospital Schleswig-Holstein, 24105 Kiel, Germany.
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14
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van Bodegraven AA, Curley CR, Hunt KA, Monsuur AJ, Linskens RK, Onnie CM, Crusius JBA, Annese V, Latiano A, Silverberg MS, Bitton A, Fisher SA, Steinhart AH, Forbes A, Sanderson J, Prescott NJ, Strachan DP, Playford RJ, Mathew CG, Wijmenga C, Daly MJ, Rioux JD, van Heel DA. Genetic variation in myosin IXB is associated with ulcerative colitis. Gastroenterology 2006; 131:1768-74. [PMID: 17087940 DOI: 10.1053/j.gastro.2006.09.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Accepted: 08/17/2006] [Indexed: 12/23/2022]
Abstract
BACKGROUND & AIMS Common germline genetic variation in the 3' region of myosin IXB (MYO9B) has been associated recently with susceptibility to celiac disease, with a hypothesis that MYO9B variants might influence intestinal permeability. These findings suggested the current study investigating a possible further role for MYO9B variation in inflammatory bowel disease. METHODS Eight single-nucleotide polymorphisms (SNPs) were selected to tag common haplotypes from the 35-kb 3' region of MYO9B. These included the strongest celiac disease-associated variants reported in a Dutch cohort. These SNPs were studied in 3 independently collected and genotyped case-control cohorts of European descent (UK, Dutch, and Canadian/Italian), comprising in total 2717 inflammatory bowel disease patients (1197 with Crohn's disease, 1520 with ulcerative colitis) and 4440 controls. RESULTS Common variation in MYO9B was associated with susceptibility to inflammatory bowel disease in all 3 cohorts examined (most associated SNP, rs1545620; meta-analysis P = 1.9 x 10(-6); odds ratio, 1.2), with the same alleles showing association as reported for celiac disease. CONCLUSIONS MYO9B genetic variants predispose to inflammatory bowel disease. Interestingly, rs1545620 is a nonsynonymous variant leading to an amino acid change (Ala1011Ser) in the third calmodulin binding IQ domain of MYO9B. Unlike previous variants (in other genes) reported to predispose to inflammatory bowel disease, the association at MYO9B was considerably stronger with ulcerative colitis, although weaker association with Crohn's disease also was observed. These data imply shared causal mechanisms underlying intestinal inflammatory diseases.
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15
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Fisher SA, Hampe J, Onnie CM, Daly MJ, Curley C, Purcell S, Sanderson J, Mansfield J, Annese V, Forbes A, Lewis CM, Schreiber S, Rioux JD, Mathew CG. Direct or indirect association in a complex disease: the role of SLC22A4 and SLC22A5 functional variants in Crohn disease. Hum Mutat 2006; 27:778-85. [PMID: 16835882 DOI: 10.1002/humu.20358] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A common haplotype spanning 250 kb on chromosome 5q31 is strongly associated with Crohn disease (CD). Recently, two functional variants within the SLC22A4 and SLC22A5 genes at this locus (IBD5), L503F (c.1507C > T) and G-207C (c.-207G > C), have been proposed to contribute directly to susceptibility to CD. However, extensive linkage disequilibrium at the IBD5 locus has complicated efforts to distinguish causal variants from association of the general risk haplotype. We genotyped the SLC22A4 and SLC22A5 variants and other polymorphisms across the risk haplotype in four populations of European origin, and applied regression-based haplotype analysis to over 1,200 fully genotyped case-control pairs, modeling case/control status on the presence of one or more SNPs to test for conditional association and to identify risk haplotypes. We found highly significant association of SNPs at the IBD5 locus with Crohn disease in all populations tested. However, the frequencies of L503F and G-207C in individuals who did not carry the general IBD5 risk haplotype were not significantly different in cases and controls, with associated disease odds ratios (ORs) of 0.90 (95% CI, 0.57-1.40) and 0.90 (95% CI, 0.65-1.23), respectively. Haplotype analysis showed that addition of the SLC22A4 and SLC22A5 variants to a null model that included the background risk haplotype did not significantly improve the model fit. In addition to the common risk haplotype, several rare haplotypes had an increased frequency in cases compared to controls. This study suggests that the molecular basis for Crohn disease susceptibility at the IBD5 locus remains to be defined, and highlights the challenge of the identification of causal variants in a complex disease in regions of extensive linkage disequilibrium.
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Affiliation(s)
- Sheila A Fisher
- Department of Medical and Molecular Genetics, King's College London School of Medicine, Guy's Hospital, London, United Kingdom
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16
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Onnie CM, Fisher SA, Pattni R, Sanderson J, Forbes A, Lewis CM, Mathew CG. Associations of allelic variants of the multidrug resistance gene (ABCB1 or MDR1) and inflammatory bowel disease and their effects on disease behavior: a case-control and meta-analysis study. Inflamm Bowel Dis 2006; 12:263-71. [PMID: 16633048 DOI: 10.1097/01.mib.0000209791.98866.ba] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Allelic variants of the ATP-binding cassette, subfamily B member 1 (ABCB1), also known as the multidrug resistance gene (MDR1) that encodes the membrane-bound efflux transporter P-glycoprotein 170 (PGP-170), have been associated with inflammatory bowel disease but with conflicting results. METHODS The present study examined the association of ABCB1 C3435T and G2677T/A in a large British case-control cohort of 828 Crohn's disease, 580 ulcerative colitis (UC) cases, and 285 healthy controls. The effect of these variants was further examined with respect to phenotypic and epidemiological characteristics. A meta-analysis was carried out of our results and those from 8 previously published association studies of the C3435T variant in inflammatory bowel disease. RESULTS The 2677T allele was significantly increased in British UC cases compared with controls (45.2% vs. 39.6%; P = 0.034). In particular, the TT genotype was significantly associated with severe UC (odds ratio [OR] 1.90; 95% CI 1.01-3.55) and the use of steroids in UC (OR 1.77; 95% CI 1.08-2.88). No significant association was seen with C3435T and UC, Crohn's disease, or any clinical subgroup. A meta-analysis of 9 association studies of C3435T showed a significant association of the 3435T allele with UC (OR 1.12; 95% CI 1.02-1.23; P = 0.013) but not with CD. CONCLUSIONS These results indicate that ABCB1 sequence variants are associated with a small increase in the risk of developing UC and may influence disease behavior.
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Affiliation(s)
- Clive M Onnie
- Department of Medical and Molecular Genetics, King's College London School of Medicine, Guy's Hospital, UK
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King K, Sheikh MF, Cuthbert AP, Fisher SA, Onnie CM, Mirza MM, Pattni RC, Sanderson J, Forbes A, Mansfield J, Lewis CM, Roberts RG, Mathew CG. Mutation, selection, and evolution of the Crohn disease susceptibility geneCARD15. Hum Mutat 2006; 27:44-54. [PMID: 16278823 DOI: 10.1002/humu.20264] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Three common mutations in the CARD15 (NOD2) gene are known to be associated with susceptibility to Crohn disease (CD), and genetic data suggest a gene dosage model with an increased risk of 2-4-fold in heterozygotes and 20-40-fold in homozygotes. However, the discovery of numerous rare variants of CARD15 indicates that some heterozygotes for the common mutations have a rare mutation on the other CARD15 allele, which would support a recessive model for CD. We addressed this issue by screening CARD15 for mutations in 100 CD patients who were heterozygous for one of the three common mutations. We also developed a strategy for evaluating potential disease susceptibility alleles (DSAs) that involves assessing the degree of evolutionary conservation of involved residues, predicted effects on protein structure and function, and genotyping in a large sample of cases and controls. The evolutionary analysis was aided by sequencing the entire coding region of CARD15 in three primates (chimp, gibbon, and tamarin) and aligning the human sequence with these and orthologs from other species. We found that 11 of the 100 CD patients screened had a second potential pathogenic mutation within the exonic and periexonic sequences examined. Assuming that there are no additional pathogenic mutations in noncoding regions, our study suggests that most carriers of the common DSAs are true heterozygotes, and supports previous evidence for a gene dosage model. Four novel nonsynonymous mutations were detected, one of which would produce premature termination of translation c.2686C>T (p.Arg896X). Two potential DSAs--c.2107C>T (p.Arg703Cys) and g.2238T>A (c.74-7T>A)--were significantly associated with CD in the case control sample. Analysis of the evolution of CARD15 revealed strong conservation of the encoded protein, with identity to the human sequence ranging from 99.1% in the chimp to 44.5% in fugu. Higher primates possess an open reading frame (ORF) upstream of the putative initiation site in other species that encodes a further 27 N-terminal amino acids, while four regions of high conservation are observed outside of the known domains of CARD15, indicative of additional residues of functional importance. The strategy developed here may have general application to the assessment of mutation pathogenicity and genetic models in other complex disorders.
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Affiliation(s)
- Kathy King
- Department of Medical and Molecular Genetics, Guy's, King's and St. Thomas' School of Medicine, King's College London, London, United Kingdom
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