1
|
Wilson PA, Santos Franco S, He L, Galwey NW, Meakin J, McIntyre R, McHugh SM, Nolan MA, Spain SL, Carlson T, Lobera M, Rubio JP, Davis B, McCarthy LC. Transcriptomic effects of rs4845604, an IBD and allergy-associated RORC variant, in stimulated ex vivo CD4+ T cells. PLoS One 2021; 16:e0258316. [PMID: 34673799 PMCID: PMC8530322 DOI: 10.1371/journal.pone.0258316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/23/2021] [Indexed: 11/18/2022] Open
Abstract
RORγt is an isoform of RORC, preferentially expressed in Th17 cells, that functions as a critical regulator of type 3 immunity. As murine Th17-driven inflammatory disease models were greatly diminished in RORC knock-out mice, this receptor was prioritised as an attractive therapeutic target for the treatment of several autoimmune diseases. Human genetic studies indicate a significant contributory role for RORC in several human disease conditions. Furthermore, genome-wide association studies (GWAS) report a significant association between inflammatory bowel disease (IBD) and the RORC regulatory variant rs4845604. To investigate if the rs4845604 variant may affect CD4+ T cell differentiation events, naïve CD4+ T cells were isolated from eighteen healthy subjects homozygous for the rs4845604 minor (A) or major (G) allele). Isolated cells from each subject were differentiated into distinct T cell lineages by culturing in either T cell maintenance medium or Th17 driving medium conditions for six days in the presence of an RORC inverse agonist (to prevent constitutive receptor activity) or an inactive diastereomer (control). Our proof of concept study indicated that genotype had no significant effect on the mean number of naïve CD4 T cells isolated, nor the frequency of Th1-like and Th17-like cells following six days of culture in any of the four culture conditions. Analysis of the derived RNA-seq count data identified genotype-driven transcriptional effects in each of the four culture conditions. Subsequent pathway enrichment analysis of these profiles reported perturbation of metabolic signalling networks, with the potential to affect the cellular detoxification response. This investigation reveals that rs4845604 genotype is associated with transcriptional effects in CD4+ T cells that may perturb immune and metabolic pathways. Most significantly, the rs4845604 GG, IBD risk associated, genotype may be associated with a differential detoxification response. This observation justifies further investigation in a larger cohort of both healthy and IBD-affected individuals.
Collapse
Affiliation(s)
- Paul A. Wilson
- Human Genetics, GlaxoSmithKline Medicine Research Centre, Stevenage, England
| | - Sara Santos Franco
- Clinical Unit Cambridge, Addenbrooke’s Centre for Clinical Investigation, GlaxoSmithKline, Cambridge, England
| | - Liu He
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Nicholas W. Galwey
- Research Statistics, GlaxoSmithKline Medicines Research Centre, Stevenage, England
| | - Jackie Meakin
- Functional Genomics, GlaxoSmithKline Medicines Research Centre, Stevenage, England
| | | | - Simon M. McHugh
- Clinical Unit Cambridge, Addenbrooke’s Centre for Clinical Investigation, GlaxoSmithKline, Cambridge, England
| | | | | | - Thaddeus Carlson
- Adaptive Immunity, GSK Pharma Research & Development, Cambridge, MA, United States of America
| | - Mercedes Lobera
- Adaptive Immunity, GSK Pharma Research & Development, Cambridge, MA, United States of America
| | - Justin P. Rubio
- Department of Pharmacology and Therapeutics, The University of Melbourne, Victoria, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria, Australia
| | - Bill Davis
- Clinical Unit Cambridge, Addenbrooke’s Centre for Clinical Investigation, GlaxoSmithKline, Cambridge, England
| | - Linda C. McCarthy
- Human Genetics, GlaxoSmithKline Medicine Research Centre, Stevenage, England
- * E-mail:
| |
Collapse
|
2
|
Sun BB, Maranville JC, Peters JE, Stacey D, Staley JR, Blackshaw J, Burgess S, Jiang T, Paige E, Surendran P, Oliver-Williams C, Kamat MA, Prins BP, Wilcox SK, Zimmerman ES, Chi A, Bansal N, Spain SL, Wood AM, Morrell NW, Bradley JR, Janjic N, Roberts DJ, Ouwehand WH, Todd JA, Soranzo N, Suhre K, Paul DS, Fox CS, Plenge RM, Danesh J, Runz H, Butterworth AS. Genomic atlas of the human plasma proteome. Nature 2018; 558:73-79. [PMID: 29875488 PMCID: PMC6697541 DOI: 10.1038/s41586-018-0175-2] [Citation(s) in RCA: 883] [Impact Index Per Article: 147.2] [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: 03/28/2017] [Accepted: 04/27/2018] [Indexed: 02/02/2023]
Abstract
Although plasma proteins have important roles in biological processes and are the direct targets of many drugs, the genetic factors that control inter-individual variation in plasma protein levels are not well understood. Here we characterize the genetic architecture of the human plasma proteome in healthy blood donors from the INTERVAL study. We identify 1,927 genetic associations with 1,478 proteins, a fourfold increase on existing knowledge, including trans associations for 1,104 proteins. To understand the consequences of perturbations in plasma protein levels, we apply an integrated approach that links genetic variation with biological pathway, disease, and drug databases. We show that protein quantitative trait loci overlap with gene expression quantitative trait loci, as well as with disease-associated loci, and find evidence that protein biomarkers have causal roles in disease using Mendelian randomization analysis. By linking genetic factors to diseases via specific proteins, our analyses highlight potential therapeutic targets, opportunities for matching existing drugs with new disease indications, and potential safety concerns for drugs under development.
Collapse
Affiliation(s)
- Benjamin B Sun
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - James E Peters
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - David Stacey
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - James R Staley
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - James Blackshaw
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Stephen Burgess
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Tao Jiang
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Ellie Paige
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Praveen Surendran
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Clare Oliver-Williams
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Homerton College, Cambridge, UK
| | - Mihir A Kamat
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Bram P Prins
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | | | - An Chi
- MRL, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Narinder Bansal
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Sarah L Spain
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Angela M Wood
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Nicholas W Morrell
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK
- Division of Respiratory Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
| | - John R Bradley
- NIHR Cambridge Biomedical Research Centre/BioResource, Cambridge University Hospitals, Cambridge, UK
| | | | - David J Roberts
- National Health Service (NHS) Blood and Transplant and Radcliffe Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, John Radcliffe Hospital, Oxford, UK
- BRC Haematology Theme and Department of Haematology, Churchill Hospital, Oxford, UK
| | - Willem H Ouwehand
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - John A Todd
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Nicole Soranzo
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Dirk S Paul
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Robert M Plenge
- MRL, Merck & Co., Inc., Kenilworth, NJ, USA
- Celgene Inc., Cambridge, MA, USA
| | - John Danesh
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK.
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
| | - Heiko Runz
- MRL, Merck & Co., Inc., Kenilworth, NJ, USA
- Biogen Inc., Cambridge, MA, USA
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
| |
Collapse
|
3
|
Dand N, Mucha S, Tsoi LC, Mahil SK, Stuart PE, Arnold A, Baurecht H, Burden AD, Callis Duffin K, Chandran V, Curtis CJ, Das S, Ellinghaus D, Ellinghaus E, Enerback C, Esko T, Gladman DD, Griffiths CEM, Gudjonsson JE, Hoffman P, Homuth G, Hüffmeier U, Krueger GG, Laudes M, Lee SH, Lieb W, Lim HW, Löhr S, Mrowietz U, Müller-Nurayid M, Nöthen M, Peters A, Rahman P, Reis A, Reynolds NJ, Rodriguez E, Schmidt CO, Spain SL, Strauch K, Tejasvi T, Voorhees JJ, Warren RB, Weichenthal M, Weidinger S, Zawistowski M, Nair RP, Capon F, Smith CH, Trembath RC, Abecasis GR, Elder JT, Franke A, Simpson MA, Barker JN. Exome-wide association study reveals novel psoriasis susceptibility locus at TNFSF15 and rare protective alleles in genes contributing to type I IFN signalling. Hum Mol Genet 2017; 26:4301-4313. [PMID: 28973304 PMCID: PMC5886170 DOI: 10.1093/hmg/ddx328] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 01/10/2017] [Revised: 08/15/2017] [Accepted: 08/18/2017] [Indexed: 02/06/2023] Open
Abstract
Psoriasis is a common inflammatory skin disorder for which multiple genetic susceptibility loci have been identified, but few resolved to specific functional variants. In this study, we sought to identify common and rare psoriasis-associated gene-centric variation. Using exome arrays we genotyped four independent cohorts, totalling 11 861 psoriasis cases and 28 610 controls, aggregating the dataset through statistical meta-analysis. Single variant analysis detected a previously unreported risk locus at TNFSF15 (rs6478108; P = 1.50 × 10-8, OR = 1.10), and association of common protein-altering variants at 11 loci previously implicated in psoriasis susceptibility. We validate previous reports of protective low-frequency protein-altering variants within IFIH1 (encoding an innate antiviral receptor) and TYK2 (encoding a Janus kinase), in each case establishing a further series of protective rare variants (minor allele frequency < 0.01) via gene-wide aggregation testing (IFIH1: pburden = 2.53 × 10-7, OR = 0.707; TYK2: pburden = 6.17 × 10-4, OR = 0.744). Both genes play significant roles in type I interferon (IFN) production and signalling. Several of the protective rare and low-frequency variants in IFIH1 and TYK2 disrupt conserved protein domains, highlighting potential mechanisms through which their effect may be exerted.
Collapse
Affiliation(s)
- Nick Dand
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Sören Mucha
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Lam C Tsoi
- Department of Dermatology
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Satveer K Mahil
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | | | - Andreas Arnold
- Clinic and Polyclinic of Dermatology, University Medicine Greifswald, Greifswald, Germany
| | - Hansjörg Baurecht
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - A David Burden
- Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | | | - Vinod Chandran
- Department of Medicine
- Department of Laboratory Medicine and Pathobiology
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Charles J Curtis
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Sayantan Das
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Charlotta Enerback
- Division of Cell Biology and Dermatology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Tõnu Esko
- Estonian Biobank, Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Dafna D Gladman
- Department of Medicine
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Christopher E M Griffiths
- Dermatology Centre, Salford Royal Hospital, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | | | - Per Hoffman
- Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Ulrike Hüffmeier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Gerald G Krueger
- Department of Dermatology, University of Utah, Salt Lake City, UT, USA
| | | | - Sang Hyuck Lee
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank PopGen, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Henry W Lim
- Department of Dermatology, Henry Ford Hospital, Detroit, MI, USA
| | - Sabine Löhr
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ulrich Mrowietz
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | | | - Markus Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Annette Peters
- Institute of Genetic Epidemiology, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Proton Rahman
- Memorial University of Newfoundland, St. John's, NL, Canada
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nick J Reynolds
- Dermatological Sciences, Institute of Cellular Medicine, Newcastle University Medical School, Newcastle upon Tyne, UK
- Department of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Elke Rodriguez
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Carsten O Schmidt
- Institute for Community Medicine, Study of Health in Pomerania/KEF, University Medicine Greifswald, Greifswald, Germany
| | - Sarah L Spain
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum Munich, Neuherberg, Germany
| | | | | | - Richard B Warren
- Dermatology Centre, Salford Road NHS Foundation Trust, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Michael Weichenthal
- Department of Dermatology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Matthew Zawistowski
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - Francesca Capon
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Catherine H Smith
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Richard C Trembath
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Goncalo R Abecasis
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - James T Elder
- Department of Dermatology
- Ann Arbor Veterans Hospital, Ann Arbor, MI, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Michael A Simpson
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Jonathan N Barker
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
| |
Collapse
|
4
|
Huang H, Fang M, Jostins L, Umićević Mirkov M, Boucher G, Anderson CA, Andersen V, Cleynen I, Cortes A, Crins F, D'Amato M, Deffontaine V, Dmitrieva J, Docampo E, Elansary M, Farh KKH, Franke A, Gori AS, Goyette P, Halfvarson J, Haritunians T, Knight J, Lawrance IC, Lees CW, Louis E, Mariman R, Meuwissen T, Mni M, Momozawa Y, Parkes M, Spain SL, Théâtre E, Trynka G, Satsangi J, van Sommeren S, Vermeire S, Xavier RJ, Weersma RK, Duerr RH, Mathew CG, Rioux JD, McGovern DPB, Cho JH, Georges M, Daly MJ, Barrett JC. Fine-mapping inflammatory bowel disease loci to single-variant resolution. Nature 2017; 547:173-178. [PMID: 28658209 PMCID: PMC5511510 DOI: 10.1038/nature22969] [Citation(s) in RCA: 355] [Impact Index Per Article: 50.7] [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] [Received: 10/17/2015] [Accepted: 05/07/2017] [Indexed: 12/19/2022]
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.
Collapse
Affiliation(s)
- Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
| | - Ming Fang
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Luke Jostins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Headington OX3 7BN, UK.,Christ Church, University of Oxford, St Aldates OX1 1DP, UK
| | - Maša Umićević Mirkov
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Gabrielle Boucher
- Research Center, Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Carl A Anderson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Vibeke Andersen
- Focused research unit for Molecular Diagnostic and Clinical Research (MOK), IRS-Center Sonderjylland, Hospital of Southern Jutland, 6200 Åbenrå, Denmark.,Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | | | - Adrian Cortes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Headington OX3 7BN, UK.,Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - François Crins
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Mauro D'Amato
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, 17176 Stockholm, Sweden.,Department of Gastrointestinal and Liver Diseases, BioDonostia Health Research Institute, 20014 San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Valérie Deffontaine
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Julia Dmitrieva
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Elisa Docampo
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Mahmoud Elansary
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Kyle Kai-How Farh
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.,Illumina, San Diego, California 92122, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Ann-Stephan Gori
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Philippe Goyette
- Research Center, Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, SE-70182 Örebro, Sweden
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Jo Knight
- Data Science Institute and Lancaster Medical School, Lancaster University, Lancaster LA1 4YG, UK
| | - Ian C Lawrance
- Centre for Inflammatory Bowel Diseases, Saint John of God Hospital, Subiaco, Western Australia 6008, Australia.,Harry Perkins Institute for Medical Research, School of Medicine and Pharmacology, University of Western Australia, Murdoch, Western Australia 6150, Australia
| | - Charlie W Lees
- Gastrointestinal Unit, Western General Hospital University of Edinburgh, Edinburgh, UK
| | - Edouard Louis
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Division of Gastroenterology, Centre Hospitalier Universitaire (CHU) de Liège, 4000 Liège, Belgium
| | - Rob Mariman
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Theo Meuwissen
- Institute of Livestock and Aquacultural Sciences, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Myriam Mni
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Yukihide Momozawa
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium.,Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Miles Parkes
- Inflammatory Bowel Disease Research Group, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Sarah L Spain
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,Open Targets, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Emilie Théâtre
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Gosia Trynka
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jack Satsangi
- Gastrointestinal Unit, Western General Hospital University of Edinburgh, Edinburgh, UK
| | - Suzanne van Sommeren
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Severine Vermeire
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium.,Division of Gastroenterology, University Hospital Gasthuisberg, 3000 Leuven, Belgium
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.,Gastroenterology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | | | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA.,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania 15261, USA
| | - Christopher G Mathew
- Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, UK.,Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada.,Faculté de Médecine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Judy H Cho
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Michel Georges
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| |
Collapse
|
5
|
Pouget JG, Gonçalves VF, Spain SL, Finucane HK, Raychaudhuri S, Kennedy JL, Knight J. Genome-Wide Association Studies Suggest Limited Immune Gene Enrichment in Schizophrenia Compared to 5 Autoimmune Diseases. Schizophr Bull 2016; 42:1176-84. [PMID: 27242348 PMCID: PMC4988748 DOI: 10.1093/schbul/sbw059] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There has been intense debate over the immunological basis of schizophrenia, and the potential utility of adjunct immunotherapies. The major histocompatibility complex is consistently the most powerful region of association in genome-wide association studies (GWASs) of schizophrenia and has been interpreted as strong genetic evidence supporting the immune hypothesis. However, global pathway analyses provide inconsistent evidence of immune involvement in schizophrenia, and it remains unclear whether genetic data support an immune etiology per se. Here we empirically test the hypothesis that variation in immune genes contributes to schizophrenia. We show that there is no enrichment of immune loci outside of the MHC region in the largest genetic study of schizophrenia conducted to date, in contrast to 5 diseases of known immune origin. Among 108 regions of the genome previously associated with schizophrenia, we identify 6 immune candidates (DPP4, HSPD1, EGR1, CLU, ESAM, NFATC3) encoding proteins with alternative, nonimmune roles in the brain. While our findings do not refute evidence that has accumulated in support of the immune hypothesis, they suggest that genetically mediated alterations in immune function may not play a major role in schizophrenia susceptibility. Instead, there may be a role for pleiotropic effects of a small number of immune genes that also regulate brain development and plasticity. Whether immune alterations drive schizophrenia progression is an important question to be addressed by future research, especially in light of the growing interest in applying immunotherapies in schizophrenia.
Collapse
Affiliation(s)
- Jennie G. Pouget
- *To whom correspondence should be addressed; Centre for Addiction and Mental Health, 250 College Street, Toronto, Ontario M5T 1R8, Canada; tel: 416-535-8501, fax: 416-979-4666, e-mail:
| | - Vanessa F. Gonçalves
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada;,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | | | - Sarah L. Spain
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK;,Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Hilary K. Finucane
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA;,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | | | | | - Jo Knight
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada;,Lancaster Medical School and Data Science Institute, Lancaster University, Lancaster, UK
| |
Collapse
|
6
|
Ellinghaus D, Jostins L, Spain SL, Cortes A, Bethune J, Han B, Park YR, Raychaudhuri S, Pouget JG, Hübenthal M, Folseraas T, Wang Y, Esko T, Metspalu A, Westra HJ, Franke L, Pers TH, Weersma RK, Collij V, D'Amato M, Halfvarson J, Jensen AB, Lieb W, Degenhardt F, Forstner AJ, Hofmann A, Schreiber S, Mrowietz U, Juran BD, Lazaridis KN, Brunak S, Dale AM, Trembath RC, Weidinger S, Weichenthal M, Ellinghaus E, Elder JT, Barker JNWN, Andreassen OA, McGovern DP, Karlsen TH, Barrett JC, Parkes M, Brown MA, Franke A. Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci. Nat Genet 2016; 48:510-8. [PMID: 26974007 PMCID: PMC4848113 DOI: 10.1038/ng.3528] [Citation(s) in RCA: 478] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 02/19/2016] [Indexed: 02/07/2023]
Abstract
We simultaneously investigated the genetic landscape of ankylosing spondylitis, Crohn's disease, psoriasis, primary sclerosing cholangitis and ulcerative colitis to investigate pleiotropy and the relationship between these clinically related diseases. Using high-density genotype data from more than 86,000 individuals of European ancestry, we identified 244 independent multidisease signals, including 27 new genome-wide significant susceptibility loci and 3 unreported shared risk loci. Complex pleiotropy was supported when contrasting multidisease signals with expression data sets from human, rat and mouse together with epigenetic and expressed enhancer profiles. The comorbidities among the five immune diseases were best explained by biological pleiotropy rather than heterogeneity (a subgroup of cases genetically identical to those with another disease, possibly owing to diagnostic misclassification, molecular subtypes or excessive comorbidity). In particular, the strong comorbidity between primary sclerosing cholangitis and inflammatory bowel disease is likely the result of a unique disease, which is genetically distinct from classical inflammatory bowel disease phenotypes.
Collapse
Affiliation(s)
- David Ellinghaus
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Luke Jostins
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Sarah L Spain
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Adrian Cortes
- Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jörn Bethune
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Buhm Han
- Department of Convergence Medicine, University of Ulsan College of Medicine and Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Yu Rang Park
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Soumya Raychaudhuri
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Division of Rheumatology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Jennie G Pouget
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Trine Folseraas
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Yunpeng Wang
- Department of Neurosciences, University of California, San Diego, La Jolla, California, USA
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Division of Endocrinology, Boston Children's Hospital, Cambridge, Massachusetts, USA.,Center for Basic and Translational Obesity Research, Boston Children's Hospital, Cambridge, Massachusetts, USA
| | | | - Harm-Jan Westra
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Division of Rheumatology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Tune H Pers
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Center for Basic and Translational Obesity Research, Boston Children's Hospital, Cambridge, Massachusetts, USA.,Novo Nordisk Foundation Centre for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.,Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Valerie Collij
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Mauro D'Amato
- Department of Bioscience and Nutrition, Karolinska Institutet, Stockholm, Sweden.,BioCruces Health Research Institute and Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Anders Boeck Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wolfgang Lieb
- Institute of Epidemiology, University Hospital Schleswig-Holstein, Kiel, Germany.,PopGen Biobank, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Andreas J Forstner
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Andrea Hofmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | | | | | | | | | | | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany.,Department of General Internal Medicine, Universitätsklinikum Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Ulrich Mrowietz
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian Albrechts University of Kiel, Kiel, Germany
| | - Brian D Juran
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic, College of Medicine, Rochester, Minnesota, USA
| | - Konstantinos N Lazaridis
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic, College of Medicine, Rochester, Minnesota, USA
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders M Dale
- Department of Neurosciences, University of California, San Diego, La Jolla, California, USA.,Department of Radiology, University of California, San Diego, La Jolla, California, USA
| | - Richard C Trembath
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Stephan Weidinger
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian Albrechts University of Kiel, Kiel, Germany
| | - Michael Weichenthal
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian Albrechts University of Kiel, Kiel, Germany
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, USA
| | - Jonathan N W N Barker
- St. John's Institute of Dermatology, Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Ole A Andreassen
- NORMENT, K.G. Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Division of Mental Health and Addiction, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Dermot P McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Los Angeles, California, USA.,Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Tom H Karlsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway.,Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Miles Parkes
- Inflammatory Bowel Disease Research Group, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Matthew A Brown
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia.,Institute of Health and Biomedical Innovation (IHBI), Faculty of Health, Queensland University of Technology (QUT), Translational Research Institute, Brisbane, Queensland, Australia
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| |
Collapse
|
7
|
Spain SL, Pedroso I, Kadeva N, Miller MB, Iacono WG, McGue M, Stergiakouli E, Smith GD, Putallaz M, Lubinski D, Meaburn EL, Plomin R, Simpson MA. A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence. Mol Psychiatry 2016; 21:1152. [PMID: 26324102 PMCID: PMC7608118 DOI: 10.1038/mp.2015.145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
8
|
Abstract
Genome-wide association studies (GWAS) have identified thousands of robust and replicable genetic associations for complex disease. However, the identification of the causal variants that underlie these associations has been more difficult. This problem of fine-mapping association signals predates GWAS, but the last few years have seen a surge of studies aimed at pinpointing causal variants using both statistical evidence from large association data sets and functional annotations of genetic variants. Combining these two approaches can often determine not only the causal variant but also the target gene. Recent contributions include analyses of custom genotyping arrays, such as the Immunochip, statistical methods to identify credible sets of causal variants and the addition of functional genomic annotations for coding and non-coding variation to help prioritize variants and discern functional consequence and hence the biological basis of disease risk.
Collapse
Affiliation(s)
- Sarah L Spain
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| |
Collapse
|
9
|
Scott IC, Rijsdijk F, Walker J, Quist J, Spain SL, Tan R, Steer S, Okada Y, Raychaudhuri S, Cope AP, Lewis CM. Do Genetic Susceptibility Variants Associate with Disease Severity in Early Active Rheumatoid Arthritis? J Rheumatol 2015; 42:1131-40. [PMID: 25979711 DOI: 10.3899/jrheum.141211] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2015] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Genetic variants affect both the development and severity of rheumatoid arthritis (RA). Recent studies have expanded the number of RA susceptibility variants. We tested the hypothesis that these associated with disease severity in a clinical trial cohort of patients with early, active RA. METHODS We evaluated 524 patients with RA enrolled in the Combination Anti-Rheumatic Drugs in Early RA (CARDERA) trials. We tested validated susceptibility variants - 69 single-nucleotide polymorphisms (SNP), 15 HLA-DRB1 alleles, and amino acid polymorphisms in 6 HLA molecule positions - for their associations with progression in Larsen scoring, 28-joint Disease Activity Scores, and Health Assessment Questionnaire (HAQ) scores over 2 years using linear mixed-effects and latent growth curve models. RESULTS HLA variants were associated with joint destruction. The *04:01 SNP (rs660895, p = 0.0003), *04:01 allele (p = 0.0002), and HLA-DRβ1 amino acids histidine at position 13 (p = 0.0005) and valine at position 11 (p = 0.0012) significantly associated with radiological progression. This association was only significant in anticitrullinated protein antibody (ACPA)-positive patients, suggesting that while their effects were not mediated by ACPA, they only predicted joint damage in ACPA-positive RA. Non-HLA variants did not associate with radiograph damage (assessed individually and cumulatively as a weighted genetic risk score). Two SNP - rs11889341 (STAT4, p = 0.0001) and rs653178 (SH2B3-PTPN11, p = 0.0004) - associated with HAQ scores over 6-24 months. CONCLUSION HLA susceptibility variants play an important role in determining radiological progression in early, active ACPA-positive RA. Genome-wide and HLA-wide analyses across large populations are required to better characterize the genetic architecture of radiological progression in RA.
Collapse
Affiliation(s)
- Ian C Scott
- From the Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, and Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, and Department of Rheumatology, King's College London, and Guy's Hospital, London, UK; Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo; Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.I.C. Scott, PhD, Clinical Research Fellow, Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London, and Guy's Hospital; F. Rijsdijk, PhD, Reader, SGDP Centre, Institute of Psychiatry, King's College London; J. Walker, PhD, Statistical Geneticist; J. Quist, PhD, MSc, Student; S.L. Spain, PhD, Research Associate, Department of Medical and Molecular Genetics, King's College London, and Guy's Hospital; R. Tan, MRes, Core Medical Trainee, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; S. Steer, PhD, Consultant Rheumatologist, Department of Rheumatology, King's College Hospital; Y. Okada, PhD, Tenure Track Junior Associate Professor, Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, and Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences; S. Raychaudhuri, PhD, Professor, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School; A.P. Cope, PhD, Professor, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; C.M. Lewis, PhD, Prof
| | - Frühling Rijsdijk
- From the Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, and Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, and Department of Rheumatology, King's College London, and Guy's Hospital, London, UK; Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo; Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.I.C. Scott, PhD, Clinical Research Fellow, Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London, and Guy's Hospital; F. Rijsdijk, PhD, Reader, SGDP Centre, Institute of Psychiatry, King's College London; J. Walker, PhD, Statistical Geneticist; J. Quist, PhD, MSc, Student; S.L. Spain, PhD, Research Associate, Department of Medical and Molecular Genetics, King's College London, and Guy's Hospital; R. Tan, MRes, Core Medical Trainee, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; S. Steer, PhD, Consultant Rheumatologist, Department of Rheumatology, King's College Hospital; Y. Okada, PhD, Tenure Track Junior Associate Professor, Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, and Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences; S. Raychaudhuri, PhD, Professor, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School; A.P. Cope, PhD, Professor, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; C.M. Lewis, PhD, Prof
| | - Jemma Walker
- From the Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, and Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, and Department of Rheumatology, King's College London, and Guy's Hospital, London, UK; Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo; Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.I.C. Scott, PhD, Clinical Research Fellow, Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London, and Guy's Hospital; F. Rijsdijk, PhD, Reader, SGDP Centre, Institute of Psychiatry, King's College London; J. Walker, PhD, Statistical Geneticist; J. Quist, PhD, MSc, Student; S.L. Spain, PhD, Research Associate, Department of Medical and Molecular Genetics, King's College London, and Guy's Hospital; R. Tan, MRes, Core Medical Trainee, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; S. Steer, PhD, Consultant Rheumatologist, Department of Rheumatology, King's College Hospital; Y. Okada, PhD, Tenure Track Junior Associate Professor, Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, and Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences; S. Raychaudhuri, PhD, Professor, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School; A.P. Cope, PhD, Professor, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; C.M. Lewis, PhD, Prof
| | - Jelmar Quist
- From the Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, and Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, and Department of Rheumatology, King's College London, and Guy's Hospital, London, UK; Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo; Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.I.C. Scott, PhD, Clinical Research Fellow, Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London, and Guy's Hospital; F. Rijsdijk, PhD, Reader, SGDP Centre, Institute of Psychiatry, King's College London; J. Walker, PhD, Statistical Geneticist; J. Quist, PhD, MSc, Student; S.L. Spain, PhD, Research Associate, Department of Medical and Molecular Genetics, King's College London, and Guy's Hospital; R. Tan, MRes, Core Medical Trainee, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; S. Steer, PhD, Consultant Rheumatologist, Department of Rheumatology, King's College Hospital; Y. Okada, PhD, Tenure Track Junior Associate Professor, Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, and Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences; S. Raychaudhuri, PhD, Professor, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School; A.P. Cope, PhD, Professor, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; C.M. Lewis, PhD, Prof
| | - Sarah L Spain
- From the Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, and Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, and Department of Rheumatology, King's College London, and Guy's Hospital, London, UK; Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo; Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.I.C. Scott, PhD, Clinical Research Fellow, Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London, and Guy's Hospital; F. Rijsdijk, PhD, Reader, SGDP Centre, Institute of Psychiatry, King's College London; J. Walker, PhD, Statistical Geneticist; J. Quist, PhD, MSc, Student; S.L. Spain, PhD, Research Associate, Department of Medical and Molecular Genetics, King's College London, and Guy's Hospital; R. Tan, MRes, Core Medical Trainee, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; S. Steer, PhD, Consultant Rheumatologist, Department of Rheumatology, King's College Hospital; Y. Okada, PhD, Tenure Track Junior Associate Professor, Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, and Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences; S. Raychaudhuri, PhD, Professor, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School; A.P. Cope, PhD, Professor, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; C.M. Lewis, PhD, Prof
| | - Rachael Tan
- From the Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, and Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, and Department of Rheumatology, King's College London, and Guy's Hospital, London, UK; Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo; Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.I.C. Scott, PhD, Clinical Research Fellow, Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London, and Guy's Hospital; F. Rijsdijk, PhD, Reader, SGDP Centre, Institute of Psychiatry, King's College London; J. Walker, PhD, Statistical Geneticist; J. Quist, PhD, MSc, Student; S.L. Spain, PhD, Research Associate, Department of Medical and Molecular Genetics, King's College London, and Guy's Hospital; R. Tan, MRes, Core Medical Trainee, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; S. Steer, PhD, Consultant Rheumatologist, Department of Rheumatology, King's College Hospital; Y. Okada, PhD, Tenure Track Junior Associate Professor, Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, and Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences; S. Raychaudhuri, PhD, Professor, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School; A.P. Cope, PhD, Professor, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; C.M. Lewis, PhD, Prof
| | - Sophia Steer
- From the Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, and Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, and Department of Rheumatology, King's College London, and Guy's Hospital, London, UK; Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo; Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.I.C. Scott, PhD, Clinical Research Fellow, Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London, and Guy's Hospital; F. Rijsdijk, PhD, Reader, SGDP Centre, Institute of Psychiatry, King's College London; J. Walker, PhD, Statistical Geneticist; J. Quist, PhD, MSc, Student; S.L. Spain, PhD, Research Associate, Department of Medical and Molecular Genetics, King's College London, and Guy's Hospital; R. Tan, MRes, Core Medical Trainee, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; S. Steer, PhD, Consultant Rheumatologist, Department of Rheumatology, King's College Hospital; Y. Okada, PhD, Tenure Track Junior Associate Professor, Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, and Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences; S. Raychaudhuri, PhD, Professor, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School; A.P. Cope, PhD, Professor, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; C.M. Lewis, PhD, Prof
| | - Yukinori Okada
- From the Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, and Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, and Department of Rheumatology, King's College London, and Guy's Hospital, London, UK; Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo; Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.I.C. Scott, PhD, Clinical Research Fellow, Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London, and Guy's Hospital; F. Rijsdijk, PhD, Reader, SGDP Centre, Institute of Psychiatry, King's College London; J. Walker, PhD, Statistical Geneticist; J. Quist, PhD, MSc, Student; S.L. Spain, PhD, Research Associate, Department of Medical and Molecular Genetics, King's College London, and Guy's Hospital; R. Tan, MRes, Core Medical Trainee, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; S. Steer, PhD, Consultant Rheumatologist, Department of Rheumatology, King's College Hospital; Y. Okada, PhD, Tenure Track Junior Associate Professor, Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, and Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences; S. Raychaudhuri, PhD, Professor, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School; A.P. Cope, PhD, Professor, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; C.M. Lewis, PhD, Prof
| | - Soumya Raychaudhuri
- From the Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, and Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, and Department of Rheumatology, King's College London, and Guy's Hospital, London, UK; Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo; Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.I.C. Scott, PhD, Clinical Research Fellow, Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London, and Guy's Hospital; F. Rijsdijk, PhD, Reader, SGDP Centre, Institute of Psychiatry, King's College London; J. Walker, PhD, Statistical Geneticist; J. Quist, PhD, MSc, Student; S.L. Spain, PhD, Research Associate, Department of Medical and Molecular Genetics, King's College London, and Guy's Hospital; R. Tan, MRes, Core Medical Trainee, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; S. Steer, PhD, Consultant Rheumatologist, Department of Rheumatology, King's College Hospital; Y. Okada, PhD, Tenure Track Junior Associate Professor, Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, and Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences; S. Raychaudhuri, PhD, Professor, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School; A.P. Cope, PhD, Professor, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; C.M. Lewis, PhD, Prof
| | - Andrew P Cope
- From the Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, and Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, and Department of Rheumatology, King's College London, and Guy's Hospital, London, UK; Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo; Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.I.C. Scott, PhD, Clinical Research Fellow, Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London, and Guy's Hospital; F. Rijsdijk, PhD, Reader, SGDP Centre, Institute of Psychiatry, King's College London; J. Walker, PhD, Statistical Geneticist; J. Quist, PhD, MSc, Student; S.L. Spain, PhD, Research Associate, Department of Medical and Molecular Genetics, King's College London, and Guy's Hospital; R. Tan, MRes, Core Medical Trainee, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; S. Steer, PhD, Consultant Rheumatologist, Department of Rheumatology, King's College Hospital; Y. Okada, PhD, Tenure Track Junior Associate Professor, Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, and Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences; S. Raychaudhuri, PhD, Professor, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School; A.P. Cope, PhD, Professor, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; C.M. Lewis, PhD, Prof
| | - Cathryn M Lewis
- From the Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, and Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, and Department of Rheumatology, King's College London, and Guy's Hospital, London, UK; Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo; Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.I.C. Scott, PhD, Clinical Research Fellow, Department of Medical and Molecular Genetics, and Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London, and Guy's Hospital; F. Rijsdijk, PhD, Reader, SGDP Centre, Institute of Psychiatry, King's College London; J. Walker, PhD, Statistical Geneticist; J. Quist, PhD, MSc, Student; S.L. Spain, PhD, Research Associate, Department of Medical and Molecular Genetics, King's College London, and Guy's Hospital; R. Tan, MRes, Core Medical Trainee, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; S. Steer, PhD, Consultant Rheumatologist, Department of Rheumatology, King's College Hospital; Y. Okada, PhD, Tenure Track Junior Associate Professor, Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, and Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences; S. Raychaudhuri, PhD, Professor, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School; A.P. Cope, PhD, Professor, Academic Department of Rheumatology, Centre for Molecular and Cellular Biology of Inflammation, King's College London; C.M. Lewis, PhD, Prof
| |
Collapse
|
10
|
Tsoi LC, Spain SL, Ellinghaus E, Stuart PE, Capon F, Knight J, Tejasvi T, Kang HM, Allen MH, Lambert S, Stoll SW, Weidinger S, Gudjonsson JE, Koks S, Kingo K, Esko T, Das S, Metspalu A, Weichenthal M, Enerback C, Krueger GG, Voorhees JJ, Chandran V, Rosen CF, Rahman P, Gladman DD, Reis A, Nair RP, Franke A, Barker JNWN, Abecasis GR, Trembath RC, Elder JT. Enhanced meta-analysis and replication studies identify five new psoriasis susceptibility loci. Nat Commun 2015; 6:7001. [PMID: 25939698 PMCID: PMC4422106 DOI: 10.1038/ncomms8001] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 03/24/2015] [Indexed: 02/06/2023] Open
Abstract
Psoriasis is a chronic autoimmune disease with complex genetic architecture. Previous genome-wide association studies (GWAS) and a recent meta-analysis using Immunochip data have uncovered 36 susceptibility loci. Here, we extend our previous meta-analysis of European ancestry by refined genotype calling and imputation and by the addition of 5,033 cases and 5,707 controls. The combined analysis, consisting of over 15,000 cases and 27,000 controls, identifies five new psoriasis susceptibility loci at genome-wide significance (P<5 × 10(-8)). The newly identified signals include two that reside in intergenic regions (1q31.1 and 5p13.1) and three residing near PLCL2 (3p24.3), NFKBIZ (3q12.3) and CAMK2G (10q22.2). We further demonstrate that NFKBIZ is a TRAF3IP2-dependent target of IL-17 signalling in human skin keratinocytes, thereby functionally linking two strong candidate genes. These results further integrate the genetics and immunology of psoriasis, suggesting new avenues for functional analysis and improved therapies.
Collapse
Affiliation(s)
- Lam C Tsoi
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Sarah L Spain
- Division of Genetics and Molecular Medicine, King's College London, London WC2R 2LS, UK.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Francesca Capon
- Division of Genetics and Molecular Medicine, King's College London, London WC2R 2LS, UK
| | - Jo Knight
- Neuroscience Research, Centre for Addiction and Mental Health, Toronto, Ontario, Canada M5T 1R8.,National Institute for Health Research (NIHR), Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Hyun M Kang
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Michael H Allen
- Division of Genetics and Molecular Medicine, King's College London, London WC2R 2LS, UK
| | - Sylviane Lambert
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Stefan W Stoll
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Stephan Weidinger
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Sulev Koks
- Department of Pathophysiology, Centre of Translational Medicine and Centre for Translational Genomics, University of Tartu, 50409 Tartu, Estonia
| | - Külli Kingo
- Department of Dermatology and Venereology, University of Tartu, 50409 Tartu, Estonia
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, 51010 Tartu, Estonia
| | - Sayantan Das
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, 51010 Tartu, Estonia
| | - Michael Weichenthal
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Charlotta Enerback
- Department of Dermatology, Linköping University, SE-581 83 Linköping, Sweden
| | - Gerald G Krueger
- Department of Dermatology, University of Utah, Salt Lake City, Utah 84132, USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Vinod Chandran
- Department of Medicine, Division of Rheumatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario, Canada M5T 2S8
| | - Cheryl F Rosen
- Department of Medicine, Division of Dermatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario, Canada M5T 2S8
| | - Proton Rahman
- Department of Medicine, Memorial University, St John's, Newfoundland, Canada A1C 5B8
| | - Dafna D Gladman
- Department of Medicine, Division of Rheumatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario, Canada M5T 2S8
| | - Andre Reis
- Institute of Human Genetics, University of Erlangen-Nuremberg, Erlangen 91054, Germany
| | - Rajan P Nair
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany
| | - Jonathan N W N Barker
- Division of Genetics and Molecular Medicine, King's College London, London WC2R 2LS, UK
| | - Goncalo R Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Richard C Trembath
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AD, UK
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan 48109, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan 48105, USA
| |
Collapse
|
11
|
Ferentinos P, Rivera M, Ising M, Spain SL, Cohen-Woods S, Butler AW, Craddock N, Owen MJ, Korszun A, Jones L, Jones I, Gill M, Rice JP, Maier W, Mors O, Rietschel M, Lucae S, Binder EB, Preisig M, Tozzi F, Muglia P, Breen G, Craig IW, Farmer AE, Müller-Myhsok B, McGuffin P, Lewis CM. Investigating the genetic variation underlying episodicity in major depressive disorder: suggestive evidence for a bipolar contribution. J Affect Disord 2014; 155:81-9. [PMID: 24215895 DOI: 10.1016/j.jad.2013.10.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 10/14/2013] [Accepted: 10/16/2013] [Indexed: 01/30/2023]
Abstract
BACKGROUND Highly recurrent major depressive disorder (MDD) has reportedly increased risk of shifting to bipolar disorder; high recurrence frequency has, therefore, featured as evidence of 'soft bipolarity'. We aimed to investigate the genetic underpinnings of total depressive episode count in recurrent MDD. METHODS Our primary sample included 1966 MDD cases with negative family history of bipolar disorder from the RADIANT studies. Total episode count was adjusted for gender, age, MDD duration, study and center before being tested for association with genotype in two separate genome-wide analyses (GWAS), in the full set and in a subset of 1364 cases with positive family history of MDD (FH+). We also calculated polygenic scores from the Psychiatric Genomics Consortium MDD and bipolar disorder studies. RESULTS Episodicity (especially intermediate episode counts) was an independent index of MDD familial aggregation, replicating previous reports. The GWAS produced no genome-wide significant findings. The strongest signals were detected in the full set at MAGI1 (p=5.1×10(-7)), previously associated with bipolar disorder, and in the FH+ subset at STIM1 (p=3.9×10(-6) after imputation), a calcium channel signaling gene. However, these findings failed to replicate in an independent Munich cohort. In the full set polygenic profile analyses, MDD polygenes predicted episodicity better than bipolar polygenes; however, in the FH+ subset, both polygenic scores performed similarly. LIMITATIONS Episode count was self-reported and, therefore, subject to recall bias. CONCLUSIONS Our findings lend preliminary support to the hypothesis that highly recurrent MDD with FH+ is part of a 'soft bipolar spectrum' but await replication in larger cohorts.
Collapse
Affiliation(s)
- Panagiotis Ferentinos
- MRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, 16 De Crespigny Park, London SE5 8AF, United Kingdom.
| | - Margarita Rivera
- MRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, 16 De Crespigny Park, London SE5 8AF, United Kingdom; Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, University of Granada, Spain
| | - Marcus Ising
- Max Planck Institute of Psychiatry, Munich, Germany
| | - Sarah L Spain
- Division of Genetics and Molecular Medicine, King's College London School of Medicine, Guy's Hospital, London, United Kingdom
| | - Sarah Cohen-Woods
- Department of Psychiatry, University of Adelaide, Adelaide, Australia
| | - Amy W Butler
- MRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, 16 De Crespigny Park, London SE5 8AF, United Kingdom; Department of Psychiatry, University of Hong Kong, Hong Kong, Special Administrative Region, China
| | - Nicholas Craddock
- MRC Centre for Neuropsychiatric Genetics and Genomics, Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Ania Korszun
- Barts and The London Medical School, Queen Mary University of London, London, United Kingdom
| | - Lisa Jones
- Department of Psychiatry, Neuropharmacology & Neurobiology Section, University of Birmingham, Birmingham, United Kingdom
| | - Ian Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Michael Gill
- Department of Psychiatry, Trinity Centre for Health Science, Dublin, Ireland
| | - John P Rice
- Department of Psychiatry, Washington University, St. Louis, Missouri, United States
| | - Wolfgang Maier
- Department of Psychiatry, University of Bonn, Bonn, Germany
| | - Ole Mors
- Centre for Psychiatric Research, Aarhus University Hospital, Risskov, Denmark
| | - Marcella Rietschel
- Division of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Mannheim, Germany
| | | | | | - Martin Preisig
- University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Federica Tozzi
- Aptuit Center for Drug Discovery & Development, Verona, Italy
| | | | - Gerome Breen
- MRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, 16 De Crespigny Park, London SE5 8AF, United Kingdom; NIHR Biomedical Research Centre for Mental Health, South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, King's College London, London, United Kingdom
| | - Ian W Craig
- MRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, 16 De Crespigny Park, London SE5 8AF, United Kingdom
| | - Anne E Farmer
- MRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, 16 De Crespigny Park, London SE5 8AF, United Kingdom
| | | | - Peter McGuffin
- MRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, 16 De Crespigny Park, London SE5 8AF, United Kingdom
| | - Cathryn M Lewis
- MRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, 16 De Crespigny Park, London SE5 8AF, United Kingdom; Division of Genetics and Molecular Medicine, King's College London School of Medicine, Guy's Hospital, London, United Kingdom
| |
Collapse
|
12
|
Palles C, Cazier JB, Howarth KM, Domingo E, Jones AM, Broderick P, Kemp Z, Spain SL, Guarino E, Salguero I, Sherborne A, Chubb D, Carvajal-Carmona LG, Ma Y, Kaur K, Dobbins S, Barclay E, Gorman M, Martin L, Kovac MB, Humphray S, Lucassen A, Holmes CC, Bentley D, Donnelly P, Taylor J, Petridis C, Roylance R, Sawyer EJ, Kerr DJ, Clark S, Grimes J, Kearsey SE, Thomas HJW, McVean G, Houlston RS, Tomlinson I. Erratum: Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas. Nat Genet 2013. [DOI: 10.1038/ng0613-713b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
13
|
Palles C, Cazier JB, Howarth KM, Domingo E, Jones AM, Broderick P, Kemp Z, Spain SL, Almeida EG, Salguero I, Sherborne A, Chubb D, Carvajal-Carmona LG, Ma Y, Kaur K, Dobbins S, Barclay E, Gorman M, Martin L, Kovac MB, Humphray S, Lucassen A, Holmes C, Bentley D, Donnelly P, Taylor J, Petridis C, Roylance R, Sawyer EJ, Kerr DJ, Clark S, Grimes J, Kearsey SE, Thomas HJW, McVean G, Houlston RS, Tomlinson I. Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas. Nat Genet 2013; 45:136-44. [PMID: 23263490 PMCID: PMC3785128 DOI: 10.1038/ng.2503] [Citation(s) in RCA: 714] [Impact Index Per Article: 64.9] [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: 08/10/2012] [Accepted: 11/28/2012] [Indexed: 12/11/2022]
Abstract
Many individuals with multiple or large colorectal adenomas or early-onset colorectal cancer (CRC) have no detectable germline mutations in the known cancer predisposition genes. Using whole-genome sequencing, supplemented by linkage and association analysis, we identified specific heterozygous POLE or POLD1 germline variants in several multiple-adenoma and/or CRC cases but in no controls. The variants associated with susceptibility, POLE p.Leu424Val and POLD1 p.Ser478Asn, have high penetrance, and POLD1 mutation was also associated with endometrial cancer predisposition. The mutations map to equivalent sites in the proofreading (exonuclease) domain of DNA polymerases ɛ and δ and are predicted to cause a defect in the correction of mispaired bases inserted during DNA replication. In agreement with this prediction, the tumors from mutation carriers were microsatellite stable but tended to acquire base substitution mutations, as confirmed by yeast functional assays. Further analysis of published data showed that the recently described group of hypermutant, microsatellite-stable CRCs is likely to be caused by somatic POLE mutations affecting the exonuclease domain.
Collapse
Affiliation(s)
- Claire Palles
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jean-Baptiste Cazier
- Bioinformatics and Statistical Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Kimberley M Howarth
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Enric Domingo
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Angela M. Jones
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Peter Broderick
- Section of Cancer Genetics, Brookes-Lawley Building, Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Zoe Kemp
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Sarah L Spain
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Estrella Guarino Almeida
- Dept. of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK
| | - Israel Salguero
- Dept. of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK
| | - Amy Sherborne
- Section of Cancer Genetics, Brookes-Lawley Building, Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Daniel Chubb
- Section of Cancer Genetics, Brookes-Lawley Building, Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Luis G Carvajal-Carmona
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Yusanne Ma
- Section of Cancer Genetics, Brookes-Lawley Building, Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Kulvinder Kaur
- Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Sara Dobbins
- Section of Cancer Genetics, Brookes-Lawley Building, Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Ella Barclay
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Maggie Gorman
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Lynn Martin
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Michal B Kovac
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Research Group Human Genetics, Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland
| | - Sean Humphray
- Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK
| | | | | | - Anneke Lucassen
- Wessex Regional Genetics, Princess Anne Hospital, Southampton SO16 5YA UK
| | - Christopher Holmes
- Bioinformatics and Statistical Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Department of Statistics, University of Oxford, South Parks Road, Oxford OX1 3TG, UK
| | - David Bentley
- Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK
| | - Peter Donnelly
- Bioinformatics and Statistical Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Department of Statistics, University of Oxford, South Parks Road, Oxford OX1 3TG, UK
| | - Jenny Taylor
- Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christos Petridis
- Guy’s, King’s, St Thomas’ Cancer Centre, Guy’s Hospital, London SE1 9RT, UK
| | - Rebecca Roylance
- Institute of Cancer, Bart’s and the London Medical School, Queen Mary College, University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Elinor J Sawyer
- Guy’s, King’s, St Thomas’ Cancer Centre, Guy’s Hospital, London SE1 9RT, UK
| | - David J. Kerr
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 7DU, UK
| | - Susan Clark
- Polyposis Registry, Imperial College School of Medicine, St Mark’s Hospital Watford Road, Harrow, HA1 3UJ, UK
| | - Jonathan Grimes
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Science Division, Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
| | - Stephen E Kearsey
- Dept. of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK
| | - Huw JW Thomas
- Family Cancer Clinic, Imperial College School of Medicine, St Mark’s Hospital Watford Road, Harrow, HA1 3UJ, UK
| | - Gilean McVean
- Bioinformatics and Statistical Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Richard S Houlston
- Section of Cancer Genetics, Brookes-Lawley Building, Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| |
Collapse
|
14
|
Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, Lee JC, Schumm LP, Sharma Y, Anderson CA, Essers J, Mitrovic M, Ning K, Cleynen I, Theatre E, Spain SL, Raychaudhuri S, Goyette P, Wei Z, Abraham C, Achkar JP, Ahmad T, Amininejad L, Ananthakrishnan AN, Andersen V, Andrews JM, Baidoo L, Balschun T, Bampton PA, Bitton A, Boucher G, Brand S, Büning C, Cohain A, Cichon S, D'Amato M, De Jong D, Devaney KL, Dubinsky M, Edwards C, Ellinghaus D, Ferguson LR, Franchimont D, Fransen K, Gearry R, Georges M, Gieger C, Glas J, Haritunians T, Hart A, Hawkey C, Hedl M, Hu X, Karlsen TH, Kupcinskas L, Kugathasan S, Latiano A, Laukens D, Lawrance IC, Lees CW, Louis E, Mahy G, Mansfield J, Morgan AR, Mowat C, Newman W, Palmieri O, Ponsioen CY, Potocnik U, Prescott NJ, Regueiro M, Rotter JI, Russell RK, Sanderson JD, Sans M, Satsangi J, Schreiber S, Simms LA, Sventoraityte J, Targan SR, Taylor KD, Tremelling M, Verspaget HW, De Vos M, Wijmenga C, Wilson DC, Winkelmann J, Xavier RJ, Zeissig S, Zhang B, Zhang CK, Zhao H, Silverberg MS, Annese V, Hakonarson H, Brant SR, Radford-Smith G, Mathew CG, Rioux JD, Schadt EE, Daly MJ, Franke A, Parkes M, Vermeire S, Barrett JC, Cho JH. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 2012; 491:119-24. [PMID: 23128233 PMCID: PMC3491803 DOI: 10.1038/nature11582] [Citation(s) in RCA: 3323] [Impact Index Per Article: 276.9] [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] [Received: 05/17/2012] [Accepted: 09/12/2012] [Indexed: 02/06/2023]
Abstract
Crohn’s disease (CD) and ulcerative colitis (UC), the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry with rising prevalence in other populations1. Genome-wide association studies (GWAS) and subsequent meta-analyses of CD and UC2,3 as separate phenotypes implicated previously unsuspected mechanisms, such as autophagy4, in pathogenesis and showed that some IBD loci are shared with other inflammatory diseases5. Here we expand knowledge of relevant pathways by undertaking a meta-analysis of CD and UC genome-wide association scans, with validation of significant findings in more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional and balancing selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe striking overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.
Collapse
Affiliation(s)
- Luke Jostins
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Tsoi LC, Spain SL, Knight J, Ellinghaus E, Stuart PE, Capon F, Ding J, Li Y, Tejasvi T, Gudjonsson JE, Kang HM, Allen MH, McManus R, Novelli G, Samuelsson L, Schalkwijk J, Ståhle M, Burden AD, Smith CH, Cork MJ, Estivill X, Bowcock AM, Krueger GG, Weger W, Worthington J, Tazi-Ahnini R, Nestle FO, Hayday A, Hoffmann P, Winkelmann J, Wijmenga C, Langford C, Edkins S, Andrews R, Blackburn H, Strange A, Band G, Pearson RD, Vukcevic D, Spencer CCA, Deloukas P, Mrowietz U, Schreiber S, Weidinger S, Koks S, Kingo K, Esko T, Metspalu A, Lim HW, Voorhees JJ, Weichenthal M, Wichmann HE, Chandran V, Rosen CF, Rahman P, Gladman DD, Griffiths CEM, Reis A, Kere J, Nair RP, Franke A, Barker JNWN, Abecasis GR, Elder JT, Trembath RC. Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity. Nat Genet 2012; 44:1341-8. [PMID: 23143594 PMCID: PMC3510312 DOI: 10.1038/ng.2467] [Citation(s) in RCA: 706] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 10/17/2012] [Indexed: 02/08/2023]
Abstract
To gain further insight into the genetic architecture of psoriasis, we conducted a meta-analysis of 3 genome-wide association studies (GWAS) and 2 independent data sets genotyped on the Immunochip, including 10,588 cases and 22,806 controls. We identified 15 new susceptibility loci, increasing to 36 the number associated with psoriasis in European individuals. We also identified, using conditional analyses, five independent signals within previously known loci. The newly identified loci shared with other autoimmune diseases include candidate genes with roles in regulating T-cell function (such as RUNX3, TAGAP and STAT3). Notably, they included candidate genes whose products are involved in innate host defense, including interferon-mediated antiviral responses (DDX58), macrophage activation (ZC3H12C) and nuclear factor (NF)-κB signaling (CARD14 and CARM1). These results portend a better understanding of shared and distinctive genetic determinants of immune-mediated inflammatory disorders and emphasize the importance of the skin in innate and acquired host defense.
Collapse
Affiliation(s)
- Lam C Tsoi
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - Sarah L Spain
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Jo Knight
- Neuroscience Research, Centre for Addiction and Mental Health, Toronto, ON, Canada M5T 1R8
- National Institute for Health Research (NIHR), Biomedical Research Centre, Guy’s and St. Thomas’ NHS Foundation Trust
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Philip E Stuart
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francesca Capon
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Jun Ding
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - Yanming Li
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - Trilokraj Tejasvi
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Hyun M Kang
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - Michael H Allen
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Ross McManus
- Department of Clinical Medicine Trinity College Dublin, Ireland
- Institute of Molecular Medicine, Trinity College Dublin, Ireland
| | - Giuseppe Novelli
- National Agency for Evaluation of Universities and Research Institutes (ANVUR)
- Research Center San Pietro Hospital, Rome, Italy
| | - Lena Samuelsson
- Department of Medical and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Joost Schalkwijk
- Department of Dermatology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Mona Ståhle
- Dermatology Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Catherine H Smith
- St John’s Institute of Dermatology, King’s College London, London, UK
| | - Michael J Cork
- Academic Unit of Dermatology Research, Department of Infection and Immunity, The University of Sheffield, Sheffield, UK
| | - Xavier Estivill
- Genes and Disease Programme, Centre for Genomic Regulation (CRG) and UPF, Hospital del Mar Research Institute (CRG) and Public Health and Epidemiology Network Biomedical Research Centre (CIBERESP), Barcelona, Spain
| | - Anne M Bowcock
- Division of Human Genetics, Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | | | - Wolfgang Weger
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - Jane Worthington
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Rachid Tazi-Ahnini
- Academic Unit of Dermatology Research, Department of Infection and Immunity, The University of Sheffield, Sheffield, UK
| | - Frank O Nestle
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Adrian Hayday
- Division of Immunology, Infection and Inflammatory Disease; King’s College London, London, UK
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, 54127 Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, 54127 Bonn, Germany
| | - Juliane Winkelmann
- Department of Neurology, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Munich, Germany
| | - Cisca Wijmenga
- Genetics Department, University Medical Center and University of Groningen, Groningen, The Netherlands
| | | | - Sarah Edkins
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | | | - Amy Strange
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | - Gavin Band
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | - Richard D Pearson
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | - Damjan Vukcevic
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | - Chris CA Spencer
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7LJ, UK
| | | | - Ulrich Mrowietz
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
- PopGen biobank, University Hospital S.-H., Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Sulev Koks
- Department of Physiology, Centre of Translational Medicine and Centre for Translational Genomics, University of Tartu, 50409 Tartu, Estonia
| | - Külli Kingo
- Department of Dermatology and Venerology, University of Tartu, 50409 Tartu, Estonia
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, 51010 Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, 51010 Tartu, Estonia
| | - Henry W Lim
- Department of Dermatology, Henry Ford Hospital, Detroit, MI, 48202, USA
| | - John J Voorhees
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michael Weichenthal
- Department of Dermatology, University Hospital, Schleswig-Holstein, Christian-Albrechts-University, 24105 Kiel, Germany
| | - H. Erich Wichmann
- Institute of Epidemiology I, Helmholtz Centre Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-University, 81377 Munich, Germany
- Klinikum Grosshadern, 81377 Munich, Germany
| | - Vinod Chandran
- Department of Medicine, Division of Rheumatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario M5T 2S8, Canada
| | - Cheryl F Rosen
- Department of Medicine, Division of Dermatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario M5T 2S8
| | - Proton Rahman
- Department of Medicine, Memorial University, St. John’s, Newfoundland A1C 5B8, Canada
| | - Dafna D Gladman
- Department of Medicine, Division of Rheumatology, University of Toronto, Toronto Western Hospital, Toronto, Ontario M5T 2S8, Canada
| | - Christopher EM Griffiths
- Dermatological Sciences, Salford Royal NHS Foundation Trust, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Andre Reis
- Institute of Human Genetics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Department of Medical Genetics, University of Helsinki, Finland
| | | | | | | | | | - Rajan P Nair
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Jonathan NWN Barker
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
- St John’s Institute of Dermatology, King’s College London, London, UK
| | - Goncalo R Abecasis
- Department of Biostatistics, Center for Statistical Genetics, University of Michigan Ann Arbor, MI 48109, USA
| | - James T Elder
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, 48105, USA
| | - Richard C Trembath
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
- Queen Mary University of London, Barts and the London School of Medicine and Dentistry, London, UK
| |
Collapse
|
16
|
Knight J, Spain SL, Capon F, Hayday A, Nestle FO, Clop A, Barker JN, Weale ME, Trembath RC. Conditional analysis identifies three novel major histocompatibility complex loci associated with psoriasis. Hum Mol Genet 2012. [PMID: 22914738 DOI: 10.1093/hmg/dds5344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Psoriasis is a common, chronic, inflammatory skin disorder. A number of genetic loci have been shown to confer risk for psoriasis. Collectively, these offer an integrated model for the inherited basis for susceptibility to psoriasis that combines altered skin barrier function together with the dysregulation of innate immune pathogen sensing and adap-tive immunity. The major histocompatibility complex (MHC) harbours the psoriasis susceptibility region which exhibits the largest effect size, driven in part by variation contained on the HLA-Cw*0602 allele. However, the resolution of the number and genomic location of potential independent risk loci are hampered by extensive linkage disequilibrium across the region. We leveraged the power of large psoriasis case and control data sets and the statistical approach of conditional analysis to identify potential further association signals distributed across the MHC. In addition to the major loci at HLA-C (P = 2.20 × 10(-236)), we observed and replicated four additional independent signals for disease association, three of which are novel. We detected evidence for association at SNPs rs2507971 (P = 6.73 × 10(-14)), rs9260313 (P = 7.93 × 10(-09)), rs66609536 (P = 3.54 × 10(-07)) and rs380924 (P = 6.24 × 10(-06)), located within the class I region of the MHC, with each observation replicated in an independent sample (P ≤ 0.01). The previously identified locus is close to MICA, the other three lie near MICB, HLA-A and HCG9 (a non-coding RNA gene). The identification of disease associations with both MICA and MICB is particularly intriguing, since each encodes an MHC class I-related protein with potent immunological function.
Collapse
Affiliation(s)
- Jo Knight
- National Institute for Health Research, Biomedical Research Centre, Guy’s and St Thomas’ NHS Foundation Trust, Toronto, ON, Canada M5T 1R8
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Knight J, Spain SL, Capon F, Hayday A, Nestle FO, Clop A, Barker JN, Weale ME, Trembath RC. Conditional analysis identifies three novel major histocompatibility complex loci associated with psoriasis. Hum Mol Genet 2012; 21:5185-92. [PMID: 22914738 DOI: 10.1093/hmg/dds344] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Psoriasis is a common, chronic, inflammatory skin disorder. A number of genetic loci have been shown to confer risk for psoriasis. Collectively, these offer an integrated model for the inherited basis for susceptibility to psoriasis that combines altered skin barrier function together with the dysregulation of innate immune pathogen sensing and adap-tive immunity. The major histocompatibility complex (MHC) harbours the psoriasis susceptibility region which exhibits the largest effect size, driven in part by variation contained on the HLA-Cw*0602 allele. However, the resolution of the number and genomic location of potential independent risk loci are hampered by extensive linkage disequilibrium across the region. We leveraged the power of large psoriasis case and control data sets and the statistical approach of conditional analysis to identify potential further association signals distributed across the MHC. In addition to the major loci at HLA-C (P = 2.20 × 10(-236)), we observed and replicated four additional independent signals for disease association, three of which are novel. We detected evidence for association at SNPs rs2507971 (P = 6.73 × 10(-14)), rs9260313 (P = 7.93 × 10(-09)), rs66609536 (P = 3.54 × 10(-07)) and rs380924 (P = 6.24 × 10(-06)), located within the class I region of the MHC, with each observation replicated in an independent sample (P ≤ 0.01). The previously identified locus is close to MICA, the other three lie near MICB, HLA-A and HCG9 (a non-coding RNA gene). The identification of disease associations with both MICA and MICB is particularly intriguing, since each encodes an MHC class I-related protein with potent immunological function.
Collapse
Affiliation(s)
- Jo Knight
- National Institute for Health Research, Biomedical Research Centre, Guy’s and St Thomas’ NHS Foundation Trust, Toronto, ON, Canada M5T 1R8
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Spain SL, Carvajal-Carmona LG, Howarth KM, Jones AM, Su Z, Cazier JB, Williams J, Aaltonen LA, Pharoah P, Kerr DJ, Cheadle J, Li L, Casey G, Vodicka P, Sieber O, Lipton L, Gibbs P, Martin NG, Montgomery GW, Young J, Baird PN, Morreau H, van Wezel T, Ruiz-Ponte C, Fernandez-Rozadilla C, Carracedo A, Castells A, Castellvi-Bel S, Dunlop M, Houlston RS, Tomlinson IPM. Refinement of the associations between risk of colorectal cancer and polymorphisms on chromosomes 1q41 and 12q13.13. Hum Mol Genet 2011; 21:934-46. [PMID: 22076443 PMCID: PMC3263985 DOI: 10.1093/hmg/ddr523] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [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: 11/18/2022] Open
Abstract
In genome-wide association studies (GWASs) of colorectal cancer, we have identified two genomic regions in which pairs of tagging-single nucleotide polymorphisms (tagSNPs) are associated with disease; these comprise chromosomes 1q41 (rs6691170, rs6687758) and 12q13.13 (rs7163702, rs11169552). We investigated these regions further, aiming to determine whether they contain more than one independent association signal and/or to identify the SNPs most strongly associated with disease. Genotyping of additional sample sets at the original tagSNPs showed that, for both regions, the two tagSNPs were unlikely to identify a single haplotype on which the functional variation lay. Conversely, one of the pair of SNPs did not fully capture the association signal in each region. We therefore undertook more detailed analyses, using imputation, logistic regression, genealogical analysis using the GENECLUSTER program and haplotype analysis. In the 1q41 region, the SNP rs11118883 emerged as a strong candidate based on all these analyses, sufficient to account for the signals at both rs6691170 and rs6687758. rs11118883 lies within a region with strong evidence of transcriptional regulatory activity and has been associated with expression of PDGFRB mRNA. For 12q13.13, a complex situation was found: SNP rs7972465 showed stronger association than either rs11169552 or rs7136702, and GENECLUSTER found no good evidence for a two-SNP model. However, logistic regression and haplotype analyses supported a two-SNP model, in which a signal at the SNP rs706793 was added to that at rs11169552. Post-GWAS fine-mapping studies are challenging, but the use of multiple tools can assist in identifying candidate functional variants in at least some cases.
Collapse
Affiliation(s)
- Sarah L Spain
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Spain SL, Cazier JB, Houlston R, Carvajal-Carmona L, Tomlinson I. Colorectal cancer risk is not associated with increased levels of homozygosity in a population from the United Kingdom. Cancer Res 2009; 69:7422-9. [PMID: 19723657 DOI: 10.1158/0008-5472.can-09-0659] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Genome-wide association studies have identified several common single nucleotide polymorphisms (SNP) associated with an increased risk of colorectal cancer (CRC), although they have failed to identify any recessively acting alleles that contribute to disease risk. However, two recent studies have suggested that inbreeding and runs of homozygosity (ROH) increase the risk of developing cancer, perhaps by exposing recessive alleles as a result of autozygosity. To examine these results in a relatively large case-control series, we analyzed samples from a cohort in the United Kingdom comprising 921 colorectal tumor cases and 929 controls. Individuals were genotyped using a 550,000 tagging SNP panel. Additionally, we identified from these SNPs a set of approximately 30,000 SNPs in low pairwise linkage disequilibrium. To determine whether homozygosity was associated with CRC, we performed multiple tests to assess homozygosity at individual SNPs and ROHs in cases and controls. No association was found between CRC and (i) homozygosity at any individual SNP, (ii) overall homozygosity or level of inbreeding, (iii) total length or number of ROHs per individual, or (iv) a ROH at any particular genomic location. In conclusion, our results from a large case-control series do not replicate those of previous studies and suggest that homozygosity/autozygosity is not a major risk factor for CRC in an outbred population.
Collapse
Affiliation(s)
- Sarah L Spain
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | | | | | | | | |
Collapse
|
20
|
Sieber OM, Segditsas S, Knudsen AL, Zhang J, Luz J, Rowan AJ, Spain SL, Thirlwell C, Howarth KM, Jaeger EEM, Robinson J, Volikos E, Silver A, Kelly G, Aretz S, Frayling I, Hutter P, Dunlop M, Guenther T, Neale K, Phillips R, Heinimann K, Tomlinson IPM. Disease severity and genetic pathways in attenuated familial adenomatous polyposis vary greatly but depend on the site of the germline mutation. Gut 2006; 55:1440-8. [PMID: 16461775 PMCID: PMC1856441 DOI: 10.1136/gut.2005.087106] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [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] [Indexed: 02/06/2023]
Abstract
BACKGROUND Attenuated familial adenomatous polyposis (AFAP) is associated with germline mutations in the 5', 3', and exon 9 of the adenomatous polyposis coli (APC) gene. These mutations probably encode a limited amount of functional APC protein. METHODS AND RESULTS We found that colonic polyp number varied greatly among AFAP patients but members of the same family tended to have more similar disease severity. 5' Mutants generally had more polyps than other patients. We analysed somatic APC mutations/loss of heterozygosity (LOH) in 235 tumours from 35 patients (16 families) with a variety of AFAP associated germline mutations. In common with two previous studies of individual kindreds, we found biallelic changes ("third hits") in some polyps. We found that the "third hit" probably initiated tumorigenesis. Somatic mutation spectra were similar in 5' and 3' mutant patients, often resembling classical FAP. In exon 9 mutants, in contrast, "third hits" were more common. Most "third hits" left three 20 amino acid repeats (20AARs) on the germline mutant APC allele, with LOH (or proximal somatic mutation) of the wild-type allele; but some polyps had loss of the germline mutant with mutation leaving one 20AAR on the wild-type allele. CONCLUSIONS We propose that mutations, such as nt4661insA, that leave three 20AARs are preferentially selected in cis with some AFAP mutations because the residual protein function is near optimal for tumorigenesis. Not all AFAP polyps appear to need "three hits" however. AFAP is phenotypically and genetically heterogeneous. In addition to effects of different germline mutations, modifier genes may be acting on the AFAP phenotype, perhaps influencing the quantity of functional protein produced by the germline mutant allele.
Collapse
Affiliation(s)
- O M Sieber
- Molecular and Population Genetics Laboratory, Cancer Research UK, London Research Institute, London, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|