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Landi MT, Bishop DT, MacGregor S, Machiela MJ, Stratigos AJ, Ghiorzo P, Brossard M, Calista D, Choi J, Fargnoli MC, Zhang T, Rodolfo M, Trower AJ, Menin C, Martinez J, Hadjisavvas A, Song L, Stefanaki I, Scolyer R, Yang R, Goldstein AM, Potrony M, Kypreou KP, Pastorino L, Queirolo P, Pellegrini C, Cattaneo L, Zawistowski M, Gimenez-Xavier P, Rodriguez A, Elefanti L, Manoukian S, Rivoltini L, Smith BH, Loizidou MA, Del Regno L, Massi D, Mandala M, Khosrotehrani K, Akslen LA, Amos CI, Andresen PA, Avril MF, Azizi E, Soyer HP, Bataille V, Dalmasso B, Bowdler LM, Burdon KP, Chen WV, Codd V, Craig JE, Dębniak T, Falchi M, Fang S, Friedman E, Simi S, Galan P, Garcia-Casado Z, Gillanders EM, Gordon S, Green A, Gruis NA, Hansson J, Harland M, Harris J, Helsing P, Henders A, Hočevar M, Höiom V, Hunter D, Ingvar C, Kumar R, Lang J, Lathrop GM, Lee JE, Li X, Lubiński J, Mackie RM, Malt M, Malvehy J, McAloney K, Mohamdi H, Molven A, Moses EK, Neale RE, Novaković S, Nyholt DR, Olsson H, Orr N, Fritsche LG, Puig-Butille JA, Qureshi AA, Radford-Smith GL, Randerson-Moor J, Requena C, Rowe C, Samani NJ, Sanna M, Schadendorf D, Schulze HJ, Simms LA, Smithers M, Song F, Swerdlow AJ, van der Stoep N, Kukutsch NA, Visconti A, Wallace L, Ward SV, Wheeler L, Sturm RA, Hutchinson A, Jones K, Malasky M, Vogt A, Zhou W, Pooley KA, Elder DE, Han J, Hicks B, Hayward NK, Kanetsky PA, Brummett C, Montgomery GW, Olsen CM, Hayward C, Dunning AM, Martin NG, Evangelou E, Mann GJ, Long G, Pharoah PDP, Easton DF, Barrett JH, Cust AE, Abecasis G, Duffy DL, Whiteman DC, Gogas H, De Nicolo A, Tucker MA, Newton-Bishop JA, Peris K, Chanock SJ, Demenais F, Brown KM, Puig S, Nagore E, Shi J, Iles MM, Law MH. Genome-wide association meta-analyses combining multiple risk phenotypes provide insights into the genetic architecture of cutaneous melanoma susceptibility. Nat Genet 2020; 52:494-504. [PMID: 32341527 PMCID: PMC7255059 DOI: 10.1038/s41588-020-0611-8] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [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: 07/10/2019] [Accepted: 03/09/2020] [Indexed: 12/17/2022]
Abstract
Most genetic susceptibility to cutaneous melanoma remains to be discovered. Meta-analysis genome-wide association study (GWAS) of 36,760 cases of melanoma (67% newly genotyped) and 375,188 controls identified 54 significant (P < 5 × 10-8) loci with 68 independent single nucleotide polymorphisms. Analysis of risk estimates across geographical regions and host factors suggests the acral melanoma subtype is uniquely unrelated to pigmentation. Combining this meta-analysis with GWAS of nevus count and hair color, and transcriptome association approaches, uncovered 31 potential secondary loci for a total of 85 cutaneous melanoma susceptibility loci. These findings provide insights into cutaneous melanoma genetic architecture, reinforcing the importance of nevogenesis, pigmentation and telomere maintenance, together with identifying potential new pathways for cutaneous melanoma pathogenesis.
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Affiliation(s)
- Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - D Timothy Bishop
- Leeds Institute of Medical Research at St James's, Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alexander J Stratigos
- Department of Dermatology, Andreas Syggros Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Paola Ghiorzo
- Genetics of Rare Cancers, Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, Genoa, Italy
| | - Myriam Brossard
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
| | - Donato Calista
- Department of Dermatology, Maurizio Bufalini Hospital, Cesena, Italy
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria Concetta Fargnoli
- Department of Dermatology & Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Monica Rodolfo
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Adam J Trower
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
| | - Chiara Menin
- Immunology and Molecular Oncology Unit, Venito Institute of Oncology IOV-IRCCS, Padua, Italy
| | | | - Andreas Hadjisavvas
- Department of EM/Molecular Pathology & The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Irene Stefanaki
- Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
| | - Richard Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
- Central Clinical School, The University of Sydney, Sydney, New South Wales, Australia
- New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - Rose Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Miriam Potrony
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, CIBERER, Barcelona, Spain
| | - Katerina P Kypreou
- Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
| | - Lorenza Pastorino
- Genetics of Rare Cancers, Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, Genoa, Italy
| | - Paola Queirolo
- Medical Oncology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Cristina Pellegrini
- Department of Dermatology & Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Laura Cattaneo
- Pathology Unit, Azienda Socio-Sanitaria Territoriale Papa Giovanni XXIII, Bergamo, Italy
| | - Matthew Zawistowski
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Pol Gimenez-Xavier
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, CIBERER, Barcelona, Spain
| | - Arantxa Rodriguez
- Department of Dermatology, Instituto Valenciano de Oncología, Valencia, Spain
| | - Lisa Elefanti
- Immunology and Molecular Oncology Unit, Venito Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Licia Rivoltini
- Unit of Immunotherapy of Human Tumors, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Maria A Loizidou
- Department of EM/Molecular Pathology & The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Laura Del Regno
- Institute of Dermatology, Catholic University, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Daniela Massi
- Section of Anatomic Pathology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Mario Mandala
- Department of Oncology, Giovanni XXIII Hospital, Bergamo, Italy
| | - Kiarash Khosrotehrani
- UQ Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
- Department of Dermatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Lars A Akslen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Christopher I Amos
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Per A Andresen
- Department of Pathology, Molecular Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Marie-Françoise Avril
- Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Service de Dermatologie, Université Paris Descartes, Paris, France
| | - Esther Azizi
- Department of Dermatology, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv, Israel
- Oncogenetics Unit, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - H Peter Soyer
- Department of Dermatology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
- Dermatology Research Centre, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Veronique Bataille
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Dermatology, West Herts NHS Trust, Herts, UK
| | - Bruna Dalmasso
- Genetics of Rare Cancers, Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, Genoa, Italy
| | - Lisa M Bowdler
- Sample Processing, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Wei V Chen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Veryan Codd
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Tadeusz Dębniak
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Dermatology, West Herts NHS Trust, Herts, UK
| | - Shenying Fang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eitan Friedman
- Oncogenetics Unit, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sarah Simi
- Section of Anatomic Pathology, Department of Health Sciences, University of Florence, Florence, Italy
| | - Pilar Galan
- Université Paris 13, Equipe de Recherche en Epidémiologie Nutritionnelle (EREN), Centre de Recherche en Epidémiologie et Statistiques, Institut National de la Santé et de la Recherche Médicale (INSERM U1153), Institut National de la Recherche Agronomique (INRA U1125), Conservatoire National des Arts et Métiers, Communauté d'Université Sorbonne Paris Cité, Bobigny, France
| | - Zaida Garcia-Casado
- Department of Dermatology, Instituto Valenciano de Oncología, Valencia, Spain
| | - Elizabeth M Gillanders
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
| | - Scott Gordon
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Adele Green
- Cancer and Population Studies, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- CRUK Manchester Institute, Institute of Inflammation and Repair, University of Manchester, Manchester, UK
| | - Nelleke A Gruis
- Department of Dermatology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Johan Hansson
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Mark Harland
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Jessica Harris
- Translational Research Institute, Institute of Health and Biomedical Innovation, Princess Alexandra Hospital, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Per Helsing
- Department of Dermatology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Anjali Henders
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Marko Hočevar
- Department of Surgical Oncology, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Veronica Höiom
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - David Hunter
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Lund University, Lund, Sweden
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Julie Lang
- Department of Medical Genetics, University of Glasgow, Glasgow, UK
| | - G Mark Lathrop
- McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | - Jeffrey E Lee
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xin Li
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Jan Lubiński
- International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Rona M Mackie
- Department of Medical Genetics, University of Glasgow, Glasgow, UK
- Department of Public Health, University of Glasgow, Glasgow, UK
| | - Maryrose Malt
- Cancer and Population Studies, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Josep Malvehy
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, CIBERER, Barcelona, Spain
| | - Kerrie McAloney
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hamida Mohamdi
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
| | - Anders Molven
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Eric K Moses
- Centre for Genetic Origins of Health and Disease, Faculty of Medicine, Dentistry and Health Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Rachel E Neale
- Cancer Aetiology & Prevention, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Srdjan Novaković
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Dale R Nyholt
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Biomedical Sciences and Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Håkan Olsson
- Department of Oncology/Pathology, Clinical Sciences, Lund University, Lund, Sweden
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Nicholas Orr
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Lars G Fritsche
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Joan Anton Puig-Butille
- Biochemistry and Molecular Genetics Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona,CIBERER, Barcelona, Spain
| | - Abrar A Qureshi
- Department of Dermatology, The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Graham L Radford-Smith
- Inflammatory Bowel Diseases, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Department of Gastroenterology and Hepatology, Royal Brisbane & Women's Hospital, Brisbane, Queensland, Australia
- University of Queensland School of Medicine, Herston Campus, Brisbane, Queensland, Australia
| | | | - Celia Requena
- Department of Dermatology, Instituto Valenciano de Oncología, Valencia, Spain
| | - Casey Rowe
- UQ Diamantina Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Marianna Sanna
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Dermatology, West Herts NHS Trust, Herts, UK
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, Essen, Germany
- German Consortium Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Hans-Joachim Schulze
- Department of Dermatology, Fachklinik Hornheide, Institute for Tumors of the Skin, University of Münster, Münster, Germany
| | - Lisa A Simms
- Inflammatory Bowel Diseases, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Mark Smithers
- Queensland Melanoma Project, Princess Alexandra Hospital, The University of Queensland, St Lucia, Queensland, Australia
- Mater Research Institute, The University of Queensland, St Lucia, Queensland, Australia
| | - Fengju Song
- Departments of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, Tianjin, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, P. R. China
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Nienke van der Stoep
- Department of Clinical Genetics, Center of Human and Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Nicole A Kukutsch
- Department of Dermatology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Alessia Visconti
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Dermatology, West Herts NHS Trust, Herts, UK
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Sarah V Ward
- Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lawrie Wheeler
- Translational Research Institute, Institute of Health and Biomedical Innovation, Princess Alexandra Hospital, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Richard A Sturm
- Dermatology Research Centre, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Michael Malasky
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Aurelie Vogt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Karen A Pooley
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - David E Elder
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jiali Han
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genome Research Laboratory, Leidos Biomedical Research, Bethesda, MD, USA
| | - Nicholas K Hayward
- Oncogenomics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Peter A Kanetsky
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Chad Brummett
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, USA
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Catherine M Olsen
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Graham J Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Centre for Cancer Research, Westmead Institute for Medical Research, Sydney, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Georgina Long
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Royal North Shore Hospital, Sydney, Australia
| | - Paul D P Pharoah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | | | - Anne E Cust
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
- Cancer Epidemiology and Prevention Research, Sydney School of Public Health, Sydney, Australia
| | - Goncalo Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - David L Duffy
- Dermatology Research Centre, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - David C Whiteman
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Helen Gogas
- First Department of Internal Medicine, Laikon General Hospital Greece, National and Kapodistrian University of Athens, Athens, Greece
| | - Arcangela De Nicolo
- Cancer Genomics Program, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Ketty Peris
- Institute of Dermatology, Catholic University, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Florence Demenais
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Susana Puig
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, CIBERER, Barcelona, Spain
| | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncología, Valencia, Spain
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark M Iles
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK.
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
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Pande M, Joon A, Brewster AM, Chen WV, Hopper JL, Eng C, Shete S, Casey G, Schumacher F, Lin Y, Harrison TA, White E, Ahsan H, Andrulis IL, Whittemore AS, John EM, Ko Win A, Makalic E, Schmidt DF, Kapuscinski MK, Ochs-Balcom HM, Gallinger S, Jenkins MA, Newcomb PA, Lindor NM, Peters U, Amos CI, Lynch PM. Genetic susceptibility markers for a breast-colorectal cancer phenotype: Exploratory results from genome-wide association studies. PLoS One 2018; 13:e0196245. [PMID: 29698419 PMCID: PMC5919670 DOI: 10.1371/journal.pone.0196245] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 01/25/2018] [Accepted: 04/09/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Clustering of breast and colorectal cancer has been observed within some families and cannot be explained by chance or known high-risk mutations in major susceptibility genes. Potential shared genetic susceptibility between breast and colorectal cancer, not explained by high-penetrance genes, has been postulated. We hypothesized that yet undiscovered genetic variants predispose to a breast-colorectal cancer phenotype. METHODS To identify variants associated with a breast-colorectal cancer phenotype, we analyzed genome-wide association study (GWAS) data from cases and controls that met the following criteria: cases (n = 985) were women with breast cancer who had one or more first- or second-degree relatives with colorectal cancer, men/women with colorectal cancer who had one or more first- or second-degree relatives with breast cancer, and women diagnosed with both breast and colorectal cancer. Controls (n = 1769), were unrelated, breast and colorectal cancer-free, and age- and sex- frequency-matched to cases. After imputation, 6,220,060 variants were analyzed using the discovery set and variants associated with the breast-colorectal cancer phenotype at P<5.0E-04 (n = 549, at 60 loci) were analyzed for replication (n = 293 cases and 2,103 controls). RESULTS Multiple correlated SNPs in intron 1 of the ROBO1 gene were suggestively associated with the breast-colorectal cancer phenotype in the discovery and replication data (most significant; rs7430339, Pdiscovery = 1.2E-04; rs7429100, Preplication = 2.8E-03). In meta-analysis of the discovery and replication data, the most significant association remained at rs7429100 (P = 1.84E-06). CONCLUSION The results of this exploratory analysis did not find clear evidence for a susceptibility locus with a pleiotropic effect on hereditary breast and colorectal cancer risk, although the suggestive association of genetic variation in the region of ROBO1, a potential tumor suppressor gene, merits further investigation.
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Affiliation(s)
- Mala Pande
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas, MD, Anderson Cancer Center, Houston, United States of America
| | - Aron Joon
- Department of Biostatistics, The University of Texas, MD, Anderson Cancer Center, Houston, TX, United States of America
| | - Abenaa M. Brewster
- Department of Clinical Cancer Prevention, The University of Texas, MD, Anderson Cancer Center, Houston, TX, United States of America
| | - Wei V. Chen
- Department of Genetics, The University of Texas, MD, Anderson Cancer Center, Houston, TX, United States of America
| | - John L. Hopper
- Epidemiology and Institute of Health and Environment, The University of Melbourne School of Population and Global Health, Parkville, VIC, Australia
| | - Cathy Eng
- Department of GI Medical Oncology, The University of Texas, MD, Anderson Cancer Center, Houston, TX, United States of America
| | - Sanjay Shete
- Department of Biostatistics, The University of Texas, MD, Anderson Cancer Center, Houston, TX, United States of America
- Department of Epidemiology, The University of Texas, MD, Anderson Cancer Center, Houston, TX, United States of America
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States of America
| | - Fredrick Schumacher
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, United States of America
| | - Yi Lin
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Tabitha A. Harrison
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Habibul Ahsan
- Department of Public Health Sciences, University of Chicago, Chicago, IL, United States of America
| | - Irene L. Andrulis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Health System, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Alice S. Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Esther M. John
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA, United States of America
- Department of Epidemiology, Cancer Prevention Institute of California, Fremont, CA, United States of America
| | - Aung Ko Win
- Epidemiology and Institute of Health and Environment, The University of Melbourne School of Population and Global Health, Parkville, VIC, Australia
| | - Enes Makalic
- Epidemiology and Institute of Health and Environment, The University of Melbourne School of Population and Global Health, Parkville, VIC, Australia
| | - Daniel F. Schmidt
- Epidemiology and Institute of Health and Environment, The University of Melbourne School of Population and Global Health, Parkville, VIC, Australia
| | - Miroslaw K. Kapuscinski
- Epidemiology and Institute of Health and Environment, The University of Melbourne School of Population and Global Health, Parkville, VIC, Australia
| | - Heather M. Ochs-Balcom
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, New York, United States of America
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Health System, Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mark A. Jenkins
- Epidemiology and Institute of Health and Environment, The University of Melbourne School of Population and Global Health, Parkville, VIC, Australia
| | - Polly A. Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Noralane M. Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, United States of America
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Christopher I. Amos
- Department of Community and Family Medicine, Dartmouth College, Lebanon, NH, United States of America
| | - Patrick M. Lynch
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas, MD, Anderson Cancer Center, Houston, United States of America
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3
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Gorlova OY, Li Y, Gorlov I, Ying J, Chen WV, Assassi S, Reveille JD, Arnett FC, Zhou X, Bossini-Castillo L, Lopez-Isac E, Acosta-Herrera M, Gregersen PK, Lee AT, Steen VD, Fessler BJ, Khanna D, Schiopu E, Silver RM, Molitor JA, Furst DE, Kafaja S, Simms RW, Lafyatis RA, Carreira P, Simeon CP, Castellvi I, Beltran E, Ortego N, Amos CI, Martin J, Mayes MD. Gene-level association analysis of systemic sclerosis: A comparison of African-Americans and White populations. PLoS One 2018; 13:e0189498. [PMID: 29293537 PMCID: PMC5749683 DOI: 10.1371/journal.pone.0189498] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/27/2017] [Indexed: 12/15/2022] Open
Abstract
Gene-level analysis of ImmunoChip or genome-wide association studies (GWAS) data has not been previously reported for systemic sclerosis (SSc, scleroderma). The objective of this study was to analyze genetic susceptibility loci in SSc at the gene level and to determine if the detected associations were shared in African-American and White populations, using data from ImmunoChip and GWAS genotyping studies. The White sample included 1833 cases and 3466 controls (956 cases and 2741 controls from the US and 877 cases and 725 controls from Spain) and the African American sample, 291 cases and 260 controls. In both Whites and African Americans, we performed a gene-level analysis that integrates association statistics in a gene possibly harboring multiple SNPs with weak effect on disease risk, using Versatile Gene-based Association Study (VEGAS) software. The SNP-level analysis was performed using PLINK v.1.07. We identified 4 novel candidate genes (STAT1, FCGR2C, NIPSNAP3B, and SCT) significantly associated and 4 genes (SERBP1, PINX1, TMEM175 and EXOC2) suggestively associated with SSc in the gene level analysis in White patients. As an exploratory analysis we compared the results on Whites with those from African Americans. Of previously established susceptibility genes identified in Whites, only TNFAIP3 was significant at the nominal level (p = 6.13x10-3) in African Americans in the gene-level analysis of the ImmunoChip data. Among the top suggestive novel genes identified in Whites based on the ImmunoChip data, FCGR2C and PINX1 were only nominally significant in African Americans (p = 0.016 and p = 0.028, respectively), while among the top novel genes identified in the gene-level analysis in African Americans, UNC5C (p = 5.57x10-4) and CLEC16A (p = 0.0463) were also nominally significant in Whites. We also present the gene-level analysis of SSc clinical and autoantibody phenotypes among Whites. Our findings need to be validated by independent studies, particularly due to the limited sample size of African Americans.
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Affiliation(s)
- Olga Y. Gorlova
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States of America
- * E-mail:
| | - Yafang Li
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States of America
| | - Ivan Gorlov
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States of America
| | - Jun Ying
- Department of Internal Medicine, Division of Rheumatology, University of Texas McGovern Medical School, Houston, TX, United States of America
| | - Wei V. Chen
- Department of Biostatistics, UT MD Anderson Cancer Center, Houston, TX, United States of America
| | - Shervin Assassi
- Department of Internal Medicine, Division of Rheumatology, University of Texas McGovern Medical School, Houston, TX, United States of America
| | - John D. Reveille
- Department of Internal Medicine, Division of Rheumatology, University of Texas McGovern Medical School, Houston, TX, United States of America
| | - Frank C. Arnett
- Department of Internal Medicine, Division of Rheumatology, University of Texas McGovern Medical School, Houston, TX, United States of America
| | - Xiaodong Zhou
- Department of Internal Medicine, Division of Rheumatology, University of Texas McGovern Medical School, Houston, TX, United States of America
| | | | - Elena Lopez-Isac
- Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, Granada, Spain
| | | | - Peter K. Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, Manhasset, NY, United States of America
| | - Annette T. Lee
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, Manhasset, NY, United States of America
| | - Virginia D. Steen
- Division of Rheumatology, Georgetown University Medical Center, Washington, D.C., United States of America
| | - Barri J. Fessler
- Division of Rheumatology, University of Alabama—Birmingham, Birmingham, AL, United States of America
| | - Dinesh Khanna
- Division of Rheumatology, University of Michigan, Ann Arbor, MI, United States of America
| | - Elena Schiopu
- Division of Rheumatology, University of Michigan, Ann Arbor, MI, United States of America
| | - Richard M. Silver
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC, United States of America
| | - Jerry A. Molitor
- Division of Rheumatic and Autoimmune Diseases, University of Minnesota, Minneapolis, MN, United States of America
| | - Daniel E. Furst
- Division of Rheumatology, University of California—Los Angeles, Los Angeles, CA, United States of America
- University of Washington, Seattle, WA, United States of America
- University of Florence, Florence, Italy
| | - Suzanne Kafaja
- Division of Rheumatology, University of California—Los Angeles, Los Angeles, CA, United States of America
| | - Robert W. Simms
- Division of Rheumatology, Boston University, Boston, MA, United States of America
| | | | | | | | | | - Emma Beltran
- Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | | | - Christopher I. Amos
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Lebanon, NH, United States of America
| | - Javier Martin
- Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, Granada, Spain
| | - Maureen D. Mayes
- Department of Internal Medicine, Division of Rheumatology, University of Texas McGovern Medical School, Houston, TX, United States of America
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4
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Haycock PC, Burgess S, Nounu A, Zheng J, Okoli GN, Bowden J, Wade KH, Timpson NJ, Evans DM, Willeit P, Aviv A, Gaunt TR, Hemani G, Mangino M, Ellis HP, Kurian KM, Pooley KA, Eeles RA, Lee JE, Fang S, Chen WV, Law MH, Bowdler LM, Iles MM, Yang Q, Worrall BB, Markus HS, Hung RJ, Amos CI, Spurdle AB, Thompson DJ, O'Mara TA, Wolpin B, Amundadottir L, Stolzenberg-Solomon R, Trichopoulou A, Onland-Moret NC, Lund E, Duell EJ, Canzian F, Severi G, Overvad K, Gunter MJ, Tumino R, Svenson U, van Rij A, Baas AF, Bown MJ, Samani NJ, van t'Hof FNG, Tromp G, Jones GT, Kuivaniemi H, Elmore JR, Johansson M, Mckay J, Scelo G, Carreras-Torres R, Gaborieau V, Brennan P, Bracci PM, Neale RE, Olson SH, Gallinger S, Li D, Petersen GM, Risch HA, Klein AP, Han J, Abnet CC, Freedman ND, Taylor PR, Maris JM, Aben KK, Kiemeney LA, Vermeulen SH, Wiencke JK, Walsh KM, Wrensch M, Rice T, Turnbull C, Litchfield K, Paternoster L, Standl M, Abecasis GR, SanGiovanni JP, Li Y, Mijatovic V, Sapkota Y, Low SK, Zondervan KT, Montgomery GW, Nyholt DR, van Heel DA, Hunt K, Arking DE, Ashar FN, Sotoodehnia N, Woo D, Rosand J, Comeau ME, Brown WM, Silverman EK, Hokanson JE, Cho MH, Hui J, Ferreira MA, Thompson PJ, Morrison AC, Felix JF, Smith NL, Christiano AM, Petukhova L, Betz RC, Fan X, Zhang X, Zhu C, Langefeld CD, Thompson SD, Wang F, Lin X, Schwartz DA, Fingerlin T, Rotter JI, Cotch MF, Jensen RA, Munz M, Dommisch H, Schaefer AS, Han F, Ollila HM, Hillary RP, Albagha O, Ralston SH, Zeng C, Zheng W, Shu XO, Reis A, Uebe S, Hüffmeier U, Kawamura Y, Otowa T, Sasaki T, Hibberd ML, Davila S, Xie G, Siminovitch K, Bei JX, Zeng YX, Försti A, Chen B, Landi S, Franke A, Fischer A, Ellinghaus D, Flores C, Noth I, Ma SF, Foo JN, Liu J, Kim JW, Cox DG, Delattre O, Mirabeau O, Skibola CF, Tang CS, Garcia-Barcelo M, Chang KP, Su WH, Chang YS, Martin NG, Gordon S, Wade TD, Lee C, Kubo M, Cha PC, Nakamura Y, Levy D, Kimura M, Hwang SJ, Hunt S, Spector T, Soranzo N, Manichaikul AW, Barr RG, Kahali B, Speliotes E, Yerges-Armstrong LM, Cheng CY, Jonas JB, Wong TY, Fogh I, Lin K, Powell JF, Rice K, Relton CL, Martin RM, Davey Smith G. Association Between Telomere Length and Risk of Cancer and Non-Neoplastic Diseases: A Mendelian Randomization Study. JAMA Oncol 2017; 3:636-651. [PMID: 28241208 PMCID: PMC5638008 DOI: 10.1001/jamaoncol.2016.5945] [Citation(s) in RCA: 287] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
IMPORTANCE The causal direction and magnitude of the association between telomere length and incidence of cancer and non-neoplastic diseases is uncertain owing to the susceptibility of observational studies to confounding and reverse causation. OBJECTIVE To conduct a Mendelian randomization study, using germline genetic variants as instrumental variables, to appraise the causal relevance of telomere length for risk of cancer and non-neoplastic diseases. DATA SOURCES Genomewide association studies (GWAS) published up to January 15, 2015. STUDY SELECTION GWAS of noncommunicable diseases that assayed germline genetic variation and did not select cohort or control participants on the basis of preexisting diseases. Of 163 GWAS of noncommunicable diseases identified, summary data from 103 were available. DATA EXTRACTION AND SYNTHESIS Summary association statistics for single nucleotide polymorphisms (SNPs) that are strongly associated with telomere length in the general population. MAIN OUTCOMES AND MEASURES Odds ratios (ORs) and 95% confidence intervals (CIs) for disease per standard deviation (SD) higher telomere length due to germline genetic variation. RESULTS Summary data were available for 35 cancers and 48 non-neoplastic diseases, corresponding to 420 081 cases (median cases, 2526 per disease) and 1 093 105 controls (median, 6789 per disease). Increased telomere length due to germline genetic variation was generally associated with increased risk for site-specific cancers. The strongest associations (ORs [95% CIs] per 1-SD change in genetically increased telomere length) were observed for glioma, 5.27 (3.15-8.81); serous low-malignant-potential ovarian cancer, 4.35 (2.39-7.94); lung adenocarcinoma, 3.19 (2.40-4.22); neuroblastoma, 2.98 (1.92-4.62); bladder cancer, 2.19 (1.32-3.66); melanoma, 1.87 (1.55-2.26); testicular cancer, 1.76 (1.02-3.04); kidney cancer, 1.55 (1.08-2.23); and endometrial cancer, 1.31 (1.07-1.61). Associations were stronger for rarer cancers and at tissue sites with lower rates of stem cell division. There was generally little evidence of association between genetically increased telomere length and risk of psychiatric, autoimmune, inflammatory, diabetic, and other non-neoplastic diseases, except for coronary heart disease (OR, 0.78 [95% CI, 0.67-0.90]), abdominal aortic aneurysm (OR, 0.63 [95% CI, 0.49-0.81]), celiac disease (OR, 0.42 [95% CI, 0.28-0.61]) and interstitial lung disease (OR, 0.09 [95% CI, 0.05-0.15]). CONCLUSIONS AND RELEVANCE It is likely that longer telomeres increase risk for several cancers but reduce risk for some non-neoplastic diseases, including cardiovascular diseases.
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Affiliation(s)
- Philip C Haycock
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, England2School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Stephen Burgess
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, England
| | - Aayah Nounu
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, England2School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Jie Zheng
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, England2School of Social and Community Medicine, University of Bristol, Bristol, England
| | - George N Okoli
- School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Jack Bowden
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, England2School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Kaitlin Hazel Wade
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, England2School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, England2School of Social and Community Medicine, University of Bristol, Bristol, England
| | - David M Evans
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, England2School of Social and Community Medicine, University of Bristol, Bristol, England4University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Peter Willeit
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, England5Department of Neurology, Innsbruck Medical University, Austria
| | - Abraham Aviv
- Center of Human Development and Aging, Department of Pediatrics, New Jersey Medical School, Rutgers, The State University of New Jersey
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, England2School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, England2School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London England8NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, England
| | - Hayley Patricia Ellis
- Brain Tumour Research Group, Institute of Clinical Neuroscience, Learning and Research Building, Southmead Hospital, University of Bristol
| | - Kathreena M Kurian
- Brain Tumour Research Group, Institute of Clinical Neuroscience, Learning and Research Building, Southmead Hospital, University of Bristol
| | - Karen A Pooley
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, England
| | - Rosalind A Eeles
- The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, England
| | - Jeffrey E Lee
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Shenying Fang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Wei V Chen
- Department of Clinical Applications & Support, The University of Texas MD Anderson Cancer Center, Houston
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Lisa M Bowdler
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Mark M Iles
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, England
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Bradford B Worrall
- Departments of Neurology and Public Health Sciences, University of Virginia Charlottesville, Virginia
| | | | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada21Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Chris I Amos
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire
| | - Amanda B Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, England
| | - Tracy A O'Mara
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Brian Wolpin
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Laufey Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Rachael Stolzenberg-Solomon
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Antonia Trichopoulou
- Hellenic Health Foundation, Athens, Greece28WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, University of Athens Medical School, Athens, Greece
| | - N Charlotte Onland-Moret
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center, Utrecht, the Netherlands
| | - Eiliv Lund
- Institute of Community Medicine, UiT The Arctic University of Norway, Tromso, Norway
| | - Eric J Duell
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gianluca Severi
- Université Paris-Saclay, Université Paris-Sud, UVSQ, CESP, INSERM, Villejuif, France34Institut Gustave Roussy, Villejuif, France35Human Genetics Foundation (HuGeF), Torino, Italy36Cancer Council Victoria and University of Melbourne, Melbourne, Australia
| | - Kim Overvad
- Department of Public Health, Section for Epidemiology, Aarhus University, Aarhus, Denmark
| | - Marc J Gunter
- School of Public Health, Imperial College London, London, England
| | - Rosario Tumino
- Cancer Registry, Azienda Ospedaliera "Civile M.P. Arezzo," Ragusa, Italy
| | - Ulrika Svenson
- Department of Medical Biosciences, Umea University, Umea, Sweden
| | - Andre van Rij
- Surgery Department, University of Otago, Dunedin, New Zealand
| | - Annette F Baas
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Matthew J Bown
- Department of Cardiovascular Sciences and the NIHR Leicester, Cardiovascular Biomedical Research Unit, University of Leicester, Glenfield Hospital, Leicester, England
| | - Nilesh J Samani
- Department of Cardiovascular Sciences and the NIHR Leicester, Cardiovascular Biomedical Research Unit, University of Leicester, Glenfield Hospital, Leicester, England
| | - Femke N G van t'Hof
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, The Netherlands
| | - Gerard Tromp
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa46The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, Pennsylvania
| | - Gregory T Jones
- Surgery Department, University of Otago, Dunedin, New Zealand
| | - Helena Kuivaniemi
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa46The Sigfried and Janet Weis Center for Research, Geisinger Health System, Danville, Pennsylvania
| | - James R Elmore
- Department of Vascular and Endovascular Surgery, Geisinger Health System, Danville, Pennsylvania
| | - Mattias Johansson
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - James Mckay
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Ghislaine Scelo
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | | | - Valerie Gaborieau
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco
| | - Rachel E Neale
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Harvey A Risch
- Yale School of Public Health, Yale School of Medicine, and Yale Cancer Center, New Haven, Connecticut
| | - Alison P Klein
- Departments of Oncology, Pathology and Epidemiology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Jiali Han
- Department of Epidemiology, Fairbanks School of Public Health, Indiana University, Indianapolis57Indiana University Melvin and Bren Simon Cancer Center, Indianapolis
| | - Christian C Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Philip R Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - John M Maris
- Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania
| | - Katja K Aben
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands61Netherlands Comprehensive Cancer Organization, Utrecht, The Netherlands
| | - Lambertus A Kiemeney
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Sita H Vermeulen
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - John K Wiencke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California63Institute of Human Genetics, University of California, San Francisco, San Francisco, California
| | - Kyle M Walsh
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California63Institute of Human Genetics, University of California, San Francisco, San Francisco, California
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California63Institute of Human Genetics, University of California, San Francisco, San Francisco, California
| | - Terri Rice
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California
| | - Clare Turnbull
- The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, England64William Harvey Research Institute, Queen Mary University, London, England
| | - Kevin Litchfield
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, England
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, England2School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Marie Standl
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | | | - John Paul SanGiovanni
- National Institute of Alcohol Abuse and Alcoholism, Laboratory of Membrane Biophysics and Biochemistry, Section on Nutritional Neuroscience, Bethesda, Maryland69Department of Biochemistry and Molecular and Cellular Biology, Georgetown School of Medicine, Washington, DC
| | - Yong Li
- Division of Genetic Epidemiology, Institute for Medical Biometry and Statistics, Faculty of Medicine, and Medical Centre, University of Freiburg, Freiburg, Germany
| | - Vladan Mijatovic
- Department of Life and Reproduction Sciences, University of Verona, Verona, Italy
| | - Yadav Sapkota
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Siew-Kee Low
- Laboratory of Statistical Analysis, Centre for Integrative Medical Sciences, The Institute of Physical and Chemical Research (RIKEN), Yokohama, Japan
| | - Krina T Zondervan
- Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, England74Nuffield Department of Obstetrics and Gynecology, University of Oxford, John Radcliffe Hospital, Oxford, England
| | | | - Dale R Nyholt
- QIMR Berghofer Medical Research Institute, Brisbane, Australia75Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - David A van Heel
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, England
| | - Karen Hunt
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, England
| | - Dan E Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Foram N Ashar
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nona Sotoodehnia
- Division of Cardiology and Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington
| | - Daniel Woo
- University of Cincinnati College of Medicine, Department of Neurology, Cincinnati, Ohio
| | - Jonathan Rosand
- Massachusetts General Hospital, Neurology, Center for Human Genetic Research, Boston, Massachusetts
| | - Mary E Comeau
- Center for Public Health Genomics, Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - W Mark Brown
- Center for Public Health Genomics, Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Jennie Hui
- Busselton Population Medical Research Institute Inc, Sir Charles Gairdner Hospital, Perth, Australia85PathWest Laboratory Medicine of Western Australia, Perth, Australia86School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Australia87School of Population Health, University of WA, Perth, Australia
| | | | - Philip J Thompson
- The Lung Health Clinic and Institute for Respiratory Health, University of Western Australia, Perth, Australia
| | - Alanna C Morrison
- Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas Health Science Center at Houston, Houston
| | - Janine F Felix
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | - Angela M Christiano
- Departments of Dermatology and Genetics & Development, Columbia University, New York, New York
| | - Lynn Petukhova
- Departments of Dermatology and Epidemiology, Columbia University, New York, New York
| | - Regina C Betz
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Xing Fan
- Institute of Dermatology & Department of Dermatology, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xuejun Zhang
- Institute of Dermatology & Department of Dermatology, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Caihong Zhu
- Institute of Dermatology & Department of Dermatology, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Carl D Langefeld
- Center for Public Health Genomics, Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Susan D Thompson
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Feijie Wang
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xu Lin
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - David A Schwartz
- Department of Medicine, School of Medicine, University of Colorado, Aurora
| | - Tasha Fingerlin
- Department of Biomedical Research, National Jewish Health Hospital, Denver, Colorado
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California101Departments of Pediatrics and Medicine, Harbor-UCLA Medical Center, Torrance, California
| | - Mary Frances Cotch
- Epidemiology Branch, Division of Epidemiology and Clinical Applications, Intramural Research Program, National Eye Institute, National Institutes of Health, Clinical Research Center, Bethesda, Maryland
| | - Richard A Jensen
- Cardiovascular Health Research Unit, University of Washington, Seattle104Department of Medicine, University of Washington, Seattle
| | - Matthias Munz
- Department of Periodontology and Synoptic Dentistry, Center for Dental and Craniofacial Sciences, Charité - University Medicine Berlin, Berlin, Germany106Institute for Integrative and Experimental Genomics, University of Lübeck, Lübeck, Germany
| | - Henrik Dommisch
- Department of Periodontology and Synoptic Dentistry, Center for Dental and Craniofacial Sciences, Charité - University Medicine Berlin, Berlin, Germany
| | - Arne S Schaefer
- Department of Periodontology and Synoptic Dentistry, Center for Dental and Craniofacial Sciences, Charité - University Medicine Berlin, Berlin, Germany
| | - Fang Han
- Department of Pulmonary Medicine, Peking University People's Hospital, Beijing, China
| | - Hanna M Ollila
- Stanford University, Center for Sleep Sciences, Palo Alto, California
| | - Ryan P Hillary
- Stanford University, Center for Sleep Sciences, Palo Alto, California
| | - Omar Albagha
- Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar110Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland
| | - Stuart H Ralston
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland
| | - Chenjie Zeng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Andre Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Steffen Uebe
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ulrike Hüffmeier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Yoshiya Kawamura
- Department of Psychiatry, Shonan Kamakura General Hospital, Kanagawa, Japan
| | - Takeshi Otowa
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan115Graduate School of Clinical Psychology, Teikyo Heisei University Major of Professional Clinical Psychology, Tokyo, Japan
| | - Tsukasa Sasaki
- Department of Physical and Health Education, Graduate School of Education, University of Tokyo, Tokyo, Japan
| | | | - Sonia Davila
- Human Genetics, Genome Institute of Singapore, Singapore
| | - Gang Xie
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada119Departments of Medicine, Immunology, Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Katherine Siminovitch
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada119Departments of Medicine, Immunology, Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jin-Xin Bei
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yi-Xin Zeng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China121Peking Union Medical College, Beijing, China
| | - Asta Försti
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany123Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden
| | - Bowang Chen
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
| | - Andre Franke
- University Hospital Schleswig-Holstein, Kiel, Germany
| | - Annegret Fischer
- University Hospital Schleswig-Holstein, Kiel, Germany126Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Tenerife, Spain128CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Imre Noth
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Shwu-Fan Ma
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Jia Nee Foo
- Human Genetics, Genome Institute of Singapore, A*STAR, Singapore
| | - Jianjun Liu
- Human Genetics, Genome Institute of Singapore, A*STAR, Singapore
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan, University School of Medicine, Gangnam-gu, Seoul, South Korea
| | - David G Cox
- Cancer Research Center of Lyon, INSERM U1052, Lyon, France
| | | | | | | | - Clara S Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Merce Garcia-Barcelo
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Kai-Ping Chang
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital at Lin-Kou, Taoyuan, Taiwan
| | - Wen-Hui Su
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital at Lin-Kou, Taoyuan, Taiwan137Department of Biomedical Sciences, Graduate Institute of Biomedical Sciences, College of Medicine, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Sun Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | | | - Scott Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Tracey D Wade
- School of Psychology, Flinders University, Adelaide, South Australia
| | - Chaeyoung Lee
- School of Systems Biomedical Science, Soongsil University, Dongjak-gu, Seoul, South Korea
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Science, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Pei-Chieng Cha
- Division of Molecular Brain Science, Kobe University Graduate School of Medicine, Kusunoki-chou, Chuo-ku, Kobe, Japan
| | - Yusuke Nakamura
- Center for Personalized Therapeutics, The University of Chicago, Chicago, Illinois
| | - Daniel Levy
- The NHLBI's Framingham Heart Study, Framingham, Massachusetts, Population Sciences Branch of the National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Masayuki Kimura
- Center of Human Development and Aging, Department of Pediatrics, New Jersey Medical School, Rutgers, The State University of New Jersey
| | - Shih-Jen Hwang
- The NHLBI's Framingham Heart Study, Framingham, Massachusetts, Population Sciences Branch of the National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Steven Hunt
- Department of Genetic Medicine, Weill Cornell Medicine in Qatar, Doha, Qatar
| | - Tim Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London England
| | - Nicole Soranzo
- Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridge, England
| | - Ani W Manichaikul
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville
| | - R Graham Barr
- Department of Medicine and Department of Epidemiology, Columbia University Medical Center, New York, New York
| | - Bratati Kahali
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor
| | - Elizabeth Speliotes
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor
| | | | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore152Department of Ophthalmology, National University of Singapore and National University Health System, Singapore153Duke-NUS Medical School, Singapore
| | - Jost B Jonas
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing, China155Department of Ophthalmology, Medical Faculty Mannheim of the Ruprecht-Karls-University Heidelberg, Mannheim, Germany
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Center, Singapore152Department of Ophthalmology, National University of Singapore and National University Health System, Singapore153Duke-NUS Medical School, Singapore
| | - Isabella Fogh
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, England
| | - Kuang Lin
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, England
| | - John F Powell
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, England
| | - Kenneth Rice
- Department of Biostatistics, University of Washington, Seattle
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, England2School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Richard M Martin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, England2School of Social and Community Medicine, University of Bristol, Bristol, England158University of Bristol/University Hospitals Bristol NHS Foundation Trust National Institute for Health Research Bristol Nutrition Biomedical Research Unit, Bristol, England
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, England2School of Social and Community Medicine, University of Bristol, Bristol, England
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Vaysse A, Fang S, Brossard M, Wei Q, Chen WV, Mohamdi H, Vincent-Fetita L, Margaritte-Jeannin P, Lavielle N, Maubec E, Lathrop M, Avril MF, Amos CI, Lee JE, Demenais F. A comprehensive genome-wide analysis of melanoma Breslow thickness identifies interaction between CDC42 and SCIN genetic variants. Int J Cancer 2016; 139:2012-20. [PMID: 27347659 PMCID: PMC5116391 DOI: 10.1002/ijc.30245] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 06/07/2016] [Indexed: 12/23/2022]
Abstract
Breslow thickness (BT) is a major prognostic factor of cutaneous melanoma (CM), the most fatal skin cancer. The genetic component of BT has only been explored by candidate gene studies with inconsistent results. Our objective was to uncover the genetic factors underlying BT using an hypothesis-free genome-wide approach. Our analysis strategy integrated a genome-wide association study (GWAS) of single nucleotide polymorphisms (SNPs) for BT followed by pathway analysis of GWAS outcomes using the gene-set enrichment analysis (GSEA) method and epistasis analysis within BT-associated pathways. This strategy was applied to two large CM datasets with Hapmap3-imputed SNP data: the French MELARISK study for discovery (966 cases) and the MD Anderson Cancer Center study (1,546 cases) for replication. While no marginal effect of individual SNPs was revealed through GWAS, three pathways, defined by gene ontology (GO) categories were significantly enriched in genes associated with BT (false discovery rate ≤5% in both studies): hormone activity, cytokine activity and myeloid cell differentiation. Epistasis analysis, within each significant GO, identified a statistically significant interaction between CDC42 and SCIN SNPs (pmeta-int =2.2 × 10(-6) , which met the overall multiple-testing corrected threshold of 2.5 × 10(-6) ). These two SNPs (and proxies) are strongly associated with CDC42 and SCIN gene expression levels and map to regulatory elements in skin cells. This interaction has important biological relevance since CDC42 and SCIN proteins have opposite effects in actin cytoskeleton organization and dynamics, a key mechanism underlying melanoma cell migration and invasion.
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Affiliation(s)
- Amaury Vaysse
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France
- Institut Universitaire d’Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Shenying Fang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Myriam Brossard
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France
- Institut Universitaire d’Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center and Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Wei V. Chen
- Laboratory Informatics System, Department of Clinical Applications & Support, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Hamida Mohamdi
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France
- Institut Universitaire d’Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | | | - Patricia Margaritte-Jeannin
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France
- Institut Universitaire d’Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Nolwenn Lavielle
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France
- Institut Universitaire d’Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Eve Maubec
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France
- AP-HP, Service de Dermatologie, Hôpital Avicenne et Université Paris 13, Bobigny, France
| | - Mark Lathrop
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | | | - Christopher I. Amos
- Department of Community and Family Medicine, Geisel College of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Jeffrey E. Lee
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Florence Demenais
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France
- Institut Universitaire d’Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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6
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Wei C, Peng B, Han Y, Chen WV, Rother J, Tomlinson GE, Boland CR, Chaussabel D, Chaussabel M, Frazier ML, Amos CI. Mutations of HNRNPA0 and WIF1 predispose members of a large family to multiple cancers. Fam Cancer 2016; 14:297-306. [PMID: 25716654 DOI: 10.1007/s10689-014-9758-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We studied a large family that presented a strong familial susceptibility to multiple early onset cancers including prostate, breast, colon, and several other uncommon cancers. Through targeted gene, linkage, and whole genome sequencing analyses, we show that the presence of a variant in the regulatory region of HNRNPA0 associated with elevated cancer incidence in this family (Hazard ratio = 7.20, p = 0.0004). Whole genome sequencing identified a second rare protein changing mutation of WIF1 that interacted with the HNRNPA0 variant resulting in extremely high risk for cancer in carriers of mutations in both genes (p = 1.98 × 10(-13)). Analysis of downstream targets of the mutations in these two genes showed that the HNRNPA0 mutation affected expression patterns in the PI3 kinase and ERK/MAPK signaling pathways, while the WIF1 variant influenced expression of genes that play a role in NAD biosynthesis. This is a first report of variation in HNRNPA0 influencing common cancers or of a striking interaction between rare variants coexisting in an extended pedigree and jointly affecting cancer risk.
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Affiliation(s)
- Chongjuan Wei
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
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7
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Wu M, Assassi S, Salazar GA, Pedroza C, Gorlova OY, Chen WV, Charles J, Taing ML, Liao K, Wigley FM, Hummers LK, Shah AA, Hinchcliff M, Khanna D, Schiopu E, Phillips K, Furst DE, Steen V, Baron M, Hudson M, Zhou X, Pope J, Jones N, Docherty P, Khalidi NA, Robinson D, Simms RW, Silver RM, Frech TM, Fessler BJ, Fritzler MJ, Molitor JA, Segal BM, Movahedian M, Martín J, Varga J, Mayes MD. Genetic susceptibility loci of idiopathic interstitial pneumonia do not represent risk for systemic sclerosis: a case control study in Caucasian patients. Arthritis Res Ther 2016; 18:20. [PMID: 26792595 PMCID: PMC4719560 DOI: 10.1186/s13075-016-0923-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 01/06/2016] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Systemic sclerosis (SSc)-related interstitial lung disease (ILD) has phenotypic similarities to lung involvement in idiopathic interstitial pneumonia (IIP). We aimed to assess whether genetic susceptibility loci recently identified in the large IIP genome-wide association studies (GWASs) were also risk loci for SSc overall or severity of ILD in SSc. METHODS A total of 2571 SSc patients and 4500 healthy controls were investigated from the US discovery GWAS and additional US replication cohorts. Thirteen IIP-related selected single nucleotide polymorphisms (SNPs) were genotyped and analyzed for their association with SSc. RESULTS We found an association of SSc with the SNP rs6793295 in the LRRC34 gene (OR = 1.14, CI 95 % 1.03 to 1.25, p value = 0.009) and rs11191865 in the OBFC1 gene (OR = 1.09, CI 95 % 1.00 to 1.19, p value = 0.043) in the discovery cohort. Additionally, rs7934606 in MUC2 (OR = 1.24, CI 95 % 1.01 to 1.52, p value = 0.037) was associated with SSc-ILD defined by imaging. However, these associations failed to replicate in the validation cohort. Furthermore, SNPs rs2076295 in DSP (β = -2.29, CI 95 % -3.85 to -0.74, p value = 0.004) rs17690703 in SPPL2C (β = 2.04, CI 95 % 0.21 to 3.88, p value = 0.029) and rs1981997 in MAPT (β = 2.26, CI 95 % 0.35 to 4.17, p value = 0.02) were associated with percent predicted forced vital capacity (FVC%) even after adjusting for the anti-topoisomerase (ATA)-positive subset. However, these associations also did not replicate in the validation cohort. CONCLUSIONS Our results add new evidence that SSc and SSc-related ILD are genetically distinct from IIP, although they share phenotypic similarities.
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Affiliation(s)
- Minghua Wu
- Division of Rheumatology and Clinical Immunogenetics, Department of Internal Medicine, University of Texas McGovern Medical School at Houston, 6431 Fannin Street, Houston, TX, 77030, USA.
| | - Shervin Assassi
- Division of Rheumatology and Clinical Immunogenetics, Department of Internal Medicine, University of Texas McGovern Medical School at Houston, 6431 Fannin Street, Houston, TX, 77030, USA.
| | - Gloria A Salazar
- Division of Rheumatology and Clinical Immunogenetics, Department of Internal Medicine, University of Texas McGovern Medical School at Houston, 6431 Fannin Street, Houston, TX, 77030, USA.
| | - Claudia Pedroza
- Department of Pediatrics, The University of Texas Mcgovern Medical School at Houston, 6431 Fannin Street, Houston, TX, 77030, USA.
| | - Olga Y Gorlova
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, 1 Rope Ferry Road, Hanover, NH, 03755, USA.
| | - Wei V Chen
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, 1 Rope Ferry Road, Hanover, NH, 03755, USA.
| | - Julio Charles
- Division of Rheumatology and Clinical Immunogenetics, Department of Internal Medicine, University of Texas McGovern Medical School at Houston, 6431 Fannin Street, Houston, TX, 77030, USA.
| | - Miranda L Taing
- Division of Rheumatology and Clinical Immunogenetics, Department of Internal Medicine, University of Texas McGovern Medical School at Houston, 6431 Fannin Street, Houston, TX, 77030, USA.
| | - Kelley Liao
- Division of Rheumatology and Clinical Immunogenetics, Department of Internal Medicine, University of Texas McGovern Medical School at Houston, 6431 Fannin Street, Houston, TX, 77030, USA.
| | - Fredrick M Wigley
- Division of Rheumatology, Johns Hopkins University School of Medicine, 5501 Hopkins Bayview circle, Baltimore, MD, 21224, USA.
| | - Laura K Hummers
- Division of Rheumatology, Johns Hopkins University School of Medicine, 5501 Hopkins Bayview circle, Baltimore, MD, 21224, USA.
| | - Ami A Shah
- Division of Rheumatology, Johns Hopkins University School of Medicine, 5501 Hopkins Bayview circle, Baltimore, MD, 21224, USA.
| | - Monique Hinchcliff
- Division of Rheumatology, Northwestern University Feinberg School of Medicine, 240 East Huron Street, Chicago, IL, 60611, USA.
| | - Dinesh Khanna
- Department of Internal Medicine, Division of Rheumatology, University of Michigan Health Center, 300 North Ingalls Street, Ann Arbor, MI, 48109, USA.
| | - Elena Schiopu
- Department of Internal Medicine, Division of Rheumatology, University of Michigan Health Center, 300 North Ingalls Street, Ann Arbor, MI, 48109, USA.
| | - Kristine Phillips
- Department of Internal Medicine, Division of Rheumatology, University of Michigan Health Center, 300 North Ingalls Street, Ann Arbor, MI, 48109, USA.
| | - Daniel E Furst
- Division of Rheumatology, University of California Los Angeles, 1000 Veterans Avenue, Los Angeles, CA, 90024, USA.
| | - Virginia Steen
- Division of Rheumatology, Georgetown University Medical Center, 3800 Reservoir Road, Washington, MD, 20007, USA.
| | - Murray Baron
- Division of Rheumatology, McGill University, 1650 Cedar Avenue, Montreal, QC, H3G 1A4, Canada.
| | - Marie Hudson
- Division of Rheumatology, McGill University, 1650 Cedar Avenue, Montreal, QC, H3G 1A4, Canada.
| | - Xiaodong Zhou
- Division of Rheumatology and Clinical Immunogenetics, Department of Internal Medicine, University of Texas McGovern Medical School at Houston, 6431 Fannin Street, Houston, TX, 77030, USA.
| | - Janet Pope
- Division of Rheumatology, St. Joseph's Health Care, University of Western Ontario, 268 Grosvenor Street, London, ON, Canada.
| | - Niall Jones
- Division of Rheumatology, University of Alberta, 11405-87 Avenue, Edmonton, AB, T6G 1C9, Canada.
| | - Peter Docherty
- Division of Rheumatology, Moncton Hospital, 135 MacBeath Avenue, Moncton, NB, E1C 6Z8, Canada.
| | - Nader A Khalidi
- Division of Rheumatology, McMaster University at Hamilton, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada.
| | - David Robinson
- Division of Rheumatology, University of Manitoba, 820 Sherbrook Street, Winnipeg, MB, R3A 1R9, Canada.
| | - Robert W Simms
- Division of Rheumatology, Boston University School of Medicine, 72 East Concord Street, Boston, MA, 02118, USA.
| | - Richard M Silver
- Division of Rheumatology, Medical University of South Carolina, 171 Ashley Avenue, Charleston, SC, 29425, USA.
| | - Tracy M Frech
- Division of Rheumatology, University of Utah, 30 North 1900 East, Salt Lake City, UT, 84132, USA.
| | - Barri J Fessler
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, 1825 University Boulevard, Birmingham, AB, 35294, USA.
| | - Marvin J Fritzler
- Division of Rheumatology, University of Calgary Cumming School of Medicine, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada.
| | - Jerry A Molitor
- Division of Rheumatology, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN, 55455, USA.
| | - Barbara M Segal
- Division of Rheumatology, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN, 55455, USA.
| | - Malahat Movahedian
- Division of Rheumatology and Clinical Immunogenetics, Department of Internal Medicine, University of Texas McGovern Medical School at Houston, 6431 Fannin Street, Houston, TX, 77030, USA.
| | - Javier Martín
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Cientıficas, C/Ventanilla 11, 18001, Granada, Spain.
| | - John Varga
- Division of Rheumatology, Northwestern University Feinberg School of Medicine, 240 East Huron Street, Chicago, IL, 60611, USA.
| | - Maureen D Mayes
- Division of Rheumatology and Clinical Immunogenetics, Department of Internal Medicine, University of Texas McGovern Medical School at Houston, 6431 Fannin Street, Houston, TX, 77030, USA.
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8
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Law MH, Bishop DT, Lee JE, Brossard M, Martin NG, Moses EK, Song F, Barrett JH, Kumar R, Easton DF, Pharoah PDP, Swerdlow AJ, Kypreou KP, Taylor JC, Harland M, Randerson-Moor J, Akslen LA, Andresen PA, Avril MF, Azizi E, Scarrà GB, Brown KM, Dębniak T, Duffy DL, Elder DE, Fang S, Friedman E, Galan P, Ghiorzo P, Gillanders EM, Goldstein AM, Gruis NA, Hansson J, Helsing P, Hočevar M, Höiom V, Ingvar C, Kanetsky PA, Chen WV, Landi MT, Lang J, Lathrop GM, Lubiński J, Mackie RM, Mann GJ, Molven A, Montgomery GW, Novaković S, Olsson H, Puig S, Puig-Butille JA, Qureshi AA, Radford-Smith GL, van der Stoep N, van Doorn R, Whiteman DC, Craig JE, Schadendorf D, Simms LA, Burdon KP, Nyholt DR, Pooley KA, Orr N, Stratigos AJ, Cust AE, Ward SV, Hayward NK, Han J, Schulze HJ, Dunning AM, Bishop JAN, Demenais F, Amos CI, MacGregor S, Iles MM. Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma. Nat Genet 2015; 47:987-995. [PMID: 26237428 PMCID: PMC4557485 DOI: 10.1038/ng.3373] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [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: 12/18/2014] [Accepted: 07/09/2015] [Indexed: 12/17/2022]
Abstract
Thirteen common susceptibility loci have been reproducibly associated with cutaneous malignant melanoma (CMM). We report the results of an international 2-stage meta-analysis of CMM genome-wide association studies (GWAS). This meta-analysis combines 11 GWAS (5 previously unpublished) and a further three stage 2 data sets, totaling 15,990 CMM cases and 26,409 controls. Five loci not previously associated with CMM risk reached genome-wide significance (P < 5 × 10(-8)), as did 2 previously reported but unreplicated loci and all 13 established loci. Newly associated SNPs fall within putative melanocyte regulatory elements, and bioinformatic and expression quantitative trait locus (eQTL) data highlight candidate genes in the associated regions, including one involved in telomere biology.
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Affiliation(s)
- Matthew H. Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - D. Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Jeffrey E. Lee
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Myriam Brossard
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR-946, Genetic Variation and Human Diseases Unit, Paris, France
- Institut Universitaire d’Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Nicholas G. Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Eric K. Moses
- Centre for Genetic Origins of Health and Disease, Faculty of Medicine, Dentistry and Health Sciences, The University of Western Australia, Western Australia, Australia
| | - Fengju Song
- Departments of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, Tianjin, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, P. R. China
| | - Jennifer H. Barrett
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Im Neuenheimer Feld 580, Heidelberg Germany
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Paul D. P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Anthony J. Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Katerina P. Kypreou
- Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
| | - John C. Taylor
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Mark Harland
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Juliette Randerson-Moor
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Lars A. Akslen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Per A. Andresen
- Department of Pathology, Molecular Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Marie-Françoise Avril
- Assistance Publique–Hôpitaux de Paris, Hôpital Cochin, Service de Dermatologie, Université Paris Descartes, Paris, France
| | - Esther Azizi
- Department of Dermatology, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv, Israel
- Oncogenetics Unit, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Giovanna Bianchi Scarrà
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
- Laboratory of Genetics of Rare Cancers, Istituto di ricovero e cura a carattere scientifico Azienda Ospedaliera Universitaria (IRCCS AOU) San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Kevin M. Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tadeusz Dębniak
- International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - David L. Duffy
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - David E. Elder
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shenying Fang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Eitan Friedman
- Oncogenetics Unit, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Pilar Galan
- Université Paris 13, Equipe de Recherche en Epidémiologie Nutritionnelle (EREN), Centre de Recherche en Epidémiologie et Statistiques, Institut National de la Santé et de la Recherche Médicale (INSERM U1153), Institut National de la Recherche Agronomique (INRA U1125), Conservatoire National des Arts et Métiers, Communauté d'Université Sorbonne Paris Cité, F-93017 Bobigny, France
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
- Laboratory of Genetics of Rare Cancers, Istituto di ricovero e cura a carattere scientifico Azienda Ospedaliera Universitaria (IRCCS AOU) San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Elizabeth M. Gillanders
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, USA
| | - Alisa M. Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Nelleke A. Gruis
- Department of Dermatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Johan Hansson
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Per Helsing
- Department of Dermatology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Marko Hočevar
- Department of Surgical Oncology, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Veronica Höiom
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Lund University, Lund, Sweden
| | - Peter A. Kanetsky
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Wei V. Chen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | | | | | | | | | | | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Julie Lang
- Department of Medical Genetics, University of Glasgow, Glasgow, UK
| | - G. Mark Lathrop
- McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | - Jan Lubiński
- International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Rona M. Mackie
- Department of Public Health, University of Glasgow, Glasgow UK
- Department of Medical Genetics, University of Glasgow, Glasgow, UK
| | - Graham J. Mann
- Centre for Cancer Research, University of Sydney at Westmead, Millennium Institute for Medical Research and Melanoma Institute Australia, Sydney, Australia
| | - Anders Molven
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Grant W. Montgomery
- Molecular Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Srdjan Novaković
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Håkan Olsson
- Department of Oncology/Pathology, Clinical Sciences, Lund University, Lund; Sweden
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Susana Puig
- Melanoma Unit, Dermatology Department & Biochemistry and Molecular Genetics Departments, Hospital Clinic, Institut de Investigacó Biomèdica August Pi Suñe, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
| | - Joan Anton Puig-Butille
- Melanoma Unit, Dermatology Department & Biochemistry and Molecular Genetics Departments, Hospital Clinic, Institut de Investigacó Biomèdica August Pi Suñe, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Raras, Instituto de Salud Carlos III, Barcelona, Spain
| | - Abrar A. Qureshi
- Department of Dermatology, The Warren Alpert Medical School of Brown University, Rhode Island, USA
| | - Graham L. Radford-Smith
- Inflammatory Bowel Diseases, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Department of Gastroenterology and Hepatology, Royal Brisbane & Women's Hospital, Brisbane, Australia
- University of Queensland School of Medicine, Herston Campus, Brisbane, Australia
| | - Nienke van der Stoep
- Department of Clinical Genetics, Center of Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - David C. Whiteman
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jamie E. Craig
- Department of Ophthalmology, Flinders University, Adelaide, Australia
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, Essen, Germany
- German Consortium Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Lisa A. Simms
- Inflammatory Bowel Diseases, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Kathryn P. Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Dale R. Nyholt
- Molecular Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Karen A. Pooley
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Nick Orr
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Alexander J. Stratigos
- Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
| | - Anne E. Cust
- Cancer Epidemiology and Services Research, Sydney School of Public Health, The University of Sydney, Australia
| | - Sarah V. Ward
- Centre for Genetic Origins of Health and Disease, Faculty of Medicine, Dentistry and Health Sciences, The University of Western Australia, Western Australia, Australia
| | - Nicholas K. Hayward
- Oncogenomics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jiali Han
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, Indiana, USA
- Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, Indiana, USA
| | - Hans-Joachim Schulze
- Department of Dermatology, Fachklinik Hornheide, Institute for Tumors of the Skin at the University of Münster, Münster, Germany
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Julia A. Newton Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Florence Demenais
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR-946, Genetic Variation and Human Diseases Unit, Paris, France
- Institut Universitaire d’Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Christopher I. Amos
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Mark M. Iles
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
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9
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Wei C, Peng B, Han Y, Chen WV, Rother J, Tomlinson GE, Richard Boland C, Chaussabel D, Frazier ML, Amos CI. Erratum to: Mutations of HNRNPA0 and WIF1 predispose members of a large family to multiple cancers. Fam Cancer 2015; 14:307. [DOI: 10.1007/s10689-015-9801-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Brossard M, Fang S, Vaysse A, Wei Q, Chen WV, Mohamdi H, Maubec E, Lavielle N, Galan P, Lathrop M, Avril MF, Lee JE, Amos CI, Demenais F. Integrated pathway and epistasis analysis reveals interactive effect of genetic variants at TERF1 and AFAP1L2 loci on melanoma risk. Int J Cancer 2015; 137:1901-1909. [PMID: 25892537 DOI: 10.1002/ijc.29570] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/12/2015] [Accepted: 03/30/2015] [Indexed: 12/18/2022]
Abstract
Genome-wide association studies (GWASs) have characterized 13 loci associated with melanoma, which only account for a small part of melanoma risk. To identify new genes with too small an effect to be detected individually but which collectively influence melanoma risk and/or show interactive effects, we used a two-step analysis strategy including pathway analysis of genome-wide SNP data, in a first step, and epistasis analysis within significant pathways, in a second step. Pathway analysis, using the gene-set enrichment analysis (GSEA) approach and the gene ontology (GO) database, was applied to the outcomes of MELARISK (3,976 subjects) and MDACC (2,827 subjects) GWASs. Cross-gene SNP-SNP interaction analysis within melanoma-associated GOs was performed using the INTERSNP software. Five GO categories were significantly enriched in genes associated with melanoma (false discovery rate ≤ 5% in both studies): response to light stimulus, regulation of mitotic cell cycle, induction of programmed cell death, cytokine activity and oxidative phosphorylation. Epistasis analysis, within each of the five significant GOs, showed significant evidence for interaction for one SNP pair at TERF1 and AFAP1L2 loci (pmeta-int = 2.0 × 10(-7) , which met both the pathway and overall multiple-testing corrected thresholds that are equal to 9.8 × 10(-7) and 2.0 × 10(-7) , respectively) and suggestive evidence for another pair involving correlated SNPs at the same loci (pmeta-int = 3.6 × 10(-6) ). This interaction has important biological relevance given the key role of TERF1 in telomere biology and the reported physical interaction between TERF1 and AFAP1L2 proteins. This finding brings a novel piece of evidence for the emerging role of telomere dysfunction into melanoma development.
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Affiliation(s)
- Myriam Brossard
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - Shenying Fang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Amaury Vaysse
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical center and Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Wei V Chen
- Laboratory Informatics System, Department of Clinical Applications & Support, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Hamida Mohamdi
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - Eve Maubec
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France.,AP-HP (Assistance Publique-Hôpitaux de Paris), Hôpital Bichat, Service de Dermatologie, Université Paris Diderot, Paris, France
| | - Nolwenn Lavielle
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - Pilar Galan
- INSERM, UMR U557; Institut national de la Recherche Agronomique,U1125; Conservatoire national des arts et métiers, Centre de Recherche en Nutrition Humaine, Ile de France, Bobigny, France
| | - Mark Lathrop
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | | | - Jeffrey E Lee
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher I Amos
- Department of Community and Family Medicine, Geisel College of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Florence Demenais
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
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11
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Wang Y, McKay JD, Rafnar T, Wang Z, Timofeeva M, Broderick P, Zong X, Laplana M, Wei Y, Han Y, Lloyd A, Delahaye-Sourdeix M, Chubb D, Gaborieau V, Wheeler W, Chatterjee N, Thorleifsson G, Sulem P, Liu G, Kaaks R, Henrion M, Kinnersley B, Vallée M, LeCalvez-Kelm F, Stevens VL, Gapstur SM, Chen WV, Zaridze D, Szeszenia-Dabrowska N, Lissowska J, Rudnai P, Fabianova E, Mates D, Bencko V, Foretova L, Janout V, Krokan HE, Gabrielsen ME, Skorpen F, Vatten L, Njølstad I, Chen C, Goodman G, Benhamou S, Vooder T, Valk K, Nelis M, Metspalu A, Lener M, Lubiński J, Johansson M, Vineis P, Agudo A, Clavel-Chapelon F, Bueno-de-Mesquita H, Trichopoulos D, Khaw KT, Johansson M, Weiderpass E, Tjønneland A, Riboli E, Lathrop M, Scelo G, Albanes D, Caporaso NE, Ye Y, Gu J, Wu X, Spitz MR, Dienemann H, Rosenberger A, Su L, Matakidou A, Eisen T, Stefansson K, Risch A, Chanock SJ, Christiani DC, Hung RJ, Brennan P, Landi MT, Houlston RS, Amos CI. Rare variants of large effect in BRCA2 and CHEK2 affect risk of lung cancer. Nat Genet 2014; 46:736-41. [PMID: 24880342 PMCID: PMC4074058 DOI: 10.1038/ng.3002] [Citation(s) in RCA: 311] [Impact Index Per Article: 31.1] [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: 09/25/2013] [Accepted: 05/08/2014] [Indexed: 12/16/2022]
Abstract
We conducted imputation to the 1000 Genomes Project of four genome-wide association studies of lung cancer in populations of European ancestry (11,348 cases and 15,861 controls) and genotyped an additional 10,246 cases and 38,295 controls for follow-up. We identified large-effect genome-wide associations for squamous lung cancer with the rare variants BRCA2 p.Lys3326X (rs11571833, odds ratio (OR) = 2.47, P = 4.74 × 10(-20)) and CHEK2 p.Ile157Thr (rs17879961, OR = 0.38, P = 1.27 × 10(-13)). We also showed an association between common variation at 3q28 (TP63, rs13314271, OR = 1.13, P = 7.22 × 10(-10)) and lung adenocarcinoma that had been previously reported only in Asians. These findings provide further evidence for inherited genetic susceptibility to lung cancer and its biological basis. Additionally, our analysis demonstrates that imputation can identify rare disease-causing variants with substantive effects on cancer risk from preexisting genome-wide association study data.
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Affiliation(s)
- Yufei Wang
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - James D. McKay
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Thorunn Rafnar
- deCODE genetics/Amgen, Sturlugata 8, 101 Reykjavik, Iceland
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer institute, NIH, DHHS, Bethesda, MD 20892-9769, USA
| | - Maria Timofeeva
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Peter Broderick
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Xuchen Zong
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital. Toronto, Canada
| | - Marina Laplana
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yongyue Wei
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, 617-432-1641, USA
| | - Younghun Han
- Center for Genomic Medicine Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, 46 Centerra Parkway, Suite 330, Lebanon, NH 03766
| | - Amy Lloyd
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | | | - Daniel Chubb
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Valerie Gaborieau
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - William Wheeler
- Information Management Services, Inc., Rockville, MD 20852, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer institute, NIH, DHHS, Bethesda, MD 20892-9769, USA
| | | | - Patrick Sulem
- deCODE genetics/Amgen, Sturlugata 8, 101 Reykjavik, Iceland
| | - Geoffrey Liu
- Princess Margaret Hospital, University Health Network, Toronto, Canada
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Marc Henrion
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Maxime Vallée
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | | | - Victoria L. Stevens
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, 30301, USA
| | - Susan M. Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, 30301, USA
| | - Wei V. Chen
- Department of Genetics, U.T. M.D. Anderson Cancer Center, Houston, TX 77030
| | - David Zaridze
- Institute of Carcinogenesis, Russian N.N. Blokhin Cancer Research Centre, 115478 Moscow, Russia
| | | | - Jolanta Lissowska
- The M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02781, Poland
| | - Peter Rudnai
- National Institute of Environmental Health, Budapest 1097, Hungary
| | - Eleonora Fabianova
- Regional Authority of Public Health, Banska’ Bystrica 97556, Slovak Republic
| | - Dana Mates
- National Institute of Public Health, Bucharest 050463, Romania
| | - Vladimir Bencko
- 1st Faculty of Medicine, Institute of Hygiene and Epidemiology, Charles University in Prague, 12800 Prague 2, Czech Republic
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno 65653, Czech Republic
| | | | - Hans E. Krokan
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim 7489, Norway
| | - Maiken Elvestad Gabrielsen
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim 7489, Norway
| | - Frank Skorpen
- Department of Laboratory Medicine, Children’s and Women’s Health, Faculty of Medicine
| | - Lars Vatten
- Department of Public Health and General Practice, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim 7489, Norway
| | - Inger Njølstad
- Department of Community Medicine, University of Tromso, Tromso 9037, Norway
| | - Chu Chen
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Gary Goodman
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Tonu Vooder
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Kristjan Valk
- Competence Centre on Reproductive Medicine and Biology, 50410 Tartu, Estonia
| | - Mari Nelis
- Estonian Genome Center, Institute of Molecular and Cell Biology, Tartu 51010, Estonia
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Andres Metspalu
- Estonian Genome Center, Institute of Molecular and Cell Biology, Tartu 51010, Estonia
| | - Marcin Lener
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Mattias Johansson
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
- HuGeF Foundation, Torino, Italy
| | - Antonio Agudo
- Unit of Nutrition, Environment and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Francoise Clavel-Chapelon
- INSERM, Centre for research in Epidemiology and Population Health (CESP), U1018, Nutrition, Hormones and Women’s Health team, F-94805, Villejuif, France
- Université Paris Sud, UMRS 1018, F-94805, Villejuif, France
- IGR, F-94805, Villejuif, France
| | - H.Bas Bueno-de-Mesquita
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre, Utrecht, The Netherlands
| | - Dimitrios Trichopoulos
- Department of Epidemiology, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
- Bureau of Epidemiologic Research, Academy of Athens, 23 Alexandroupoleos Street, Athens, GR-115 27, Greece
- Hellenic Health Foundation, 13 Kaisareias Street, Athens, GR-115 27, Greece
| | - Kay-Tee Khaw
- University of Cambridge School of Clinical Medicine, Clinical Gerontology Unit Box 251, Addenbrooke’s Hospital, Cambridge CB2 2QQ, UK
| | - Mikael Johansson
- Department of Radiation Sciences, Umeå universitet, SE-901 87 Umeå, Sverige, Sweden
| | - Elisabete Weiderpass
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
- Department of Research, Cancer Registry of Norway, Oslo, Norway
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Samfundet Folkhälsan, Helsinki, Finland
| | - Anne Tjønneland
- Danish Cancer Society Research Center, Strandboulevarden 49, DK 2100 Copenhagen Ø, Denmark
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
| | - Mark Lathrop
- Centre d’Etude du Polymorphisme Humain (CEPH), Paris 75010, France
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer institute, NIH, DHHS, Bethesda, MD 20892-9769, USA
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer institute, NIH, DHHS, Bethesda, MD 20892-9769, USA
| | - Yuanqing Ye
- Department of Epidemiology, U.T. M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Jian Gu
- Department of Epidemiology, U.T. M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Xifeng Wu
- Department of Epidemiology, U.T. M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Margaret R. Spitz
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hendrik Dienemann
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Thoracic Surgery, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Albert Rosenberger
- Department of Genetic Epidemiology, University of Göttingen, Göttingen, Germany
| | - Li Su
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, 617-432-1641, USA
| | - Athena Matakidou
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Timothy Eisen
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Addenbrooke’s Hospital, Cambridge Biomedical Campus, Hill’s Road Cambridge CB2 0QQ, UK
| | | | - Angela Risch
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer institute, NIH, DHHS, Bethesda, MD 20892-9769, USA
| | - David C. Christiani
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, 617-432-1641, USA
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital. Toronto, Canada
| | - Paul Brennan
- International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer institute, NIH, DHHS, Bethesda, MD 20892-9769, USA
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Christopher I. Amos
- Center for Genomic Medicine Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, 46 Centerra Parkway, Suite 330, Lebanon, NH 03766
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12
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Qian J, Liu H, Wei S, Liu Z, Li Y, Wang LE, Chen WV, Amos CI, Lee JE, Iles MM, Law MH, Cust AE, Barrett JH, Montgomery GW, Taylor J, Bishop JAN, Macgregor S, Bishop DT, Mann GJ, Hayward NK, Wei Q. Association between putative functional variants in the PSMB9 gene and risk of melanoma--re-analysis of published melanoma genome-wide association studies. Pigment Cell Melanoma Res 2013; 26:392-401. [PMID: 23360169 DOI: 10.1111/pcmr.12069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 01/21/2013] [Indexed: 01/13/2023]
Abstract
To mine possibly hidden causal single-nucleotide polymorphisms (SNPs) of melanoma, we investigated the association of SNPs in 76 M/G1 transition genes with melanoma risk using our published genome-wide association study (GWAS) data set with 1804 melanoma cases and 1026 cancer-free controls. We found multiple SNPs with P < 0.01 and performed validation studies for 18 putative functional SNPs in PSMB9 in two other GWAS data sets. Two SNPs (rs1351383 and rs2127675) were associated with melanoma risk in the GenoMEL data set (P = 0.013 and 0.004, respectively), but failed in validation using the Australian data set. Genotype-phenotype analysis revealed these two SNPs were significantly correlated with mRNA expression level of PSMB9. Further experiments revealed that SNP rs2071480, which is in high LD with rs1351383 and rs2127675, may have a weak effect on the promoter activity of PSMB9. Taken together, our data suggested that functional variants in PSMB9 may contribute to melanoma susceptibility.
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Affiliation(s)
- Ji Qian
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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13
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Liu H, Wang LE, Liu Z, Chen WV, Amos CI, Lee JE, Iles MM, Law MH, Barrett JH, Montgomery GW, Taylor JC, MacGregor S, Cust AE, Newton Bishop JA, Hayward NK, Bishop DT, Mann GJ, Affleck P, Wei Q. Association between functional polymorphisms in genes involved in the MAPK signaling pathways and cutaneous melanoma risk. Carcinogenesis 2013; 34:885-92. [PMID: 23291271 DOI: 10.1093/carcin/bgs407] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Genome-wide association studies (GWASs) have mainly focused on top significant single nucleotide polymorphisms (SNPs), most of which did not have clear biological functions but were just surrogates for unknown causal variants. Studying SNPs with modest association and putative functions in biologically plausible pathways has become one complementary approach to GWASs. To unravel the key roles of mitogen-activated protein kinase (MAPK) pathways in cutaneous melanoma (CM) risk, we re-evaluated the associations between 47 818 SNPs in 280 MAPK genes and CM risk using our published GWAS dataset with 1804 CM cases and 1026 controls. We initially found 105 SNPs with P ≤ 0.001, more than expected by chance, 26 of which were predicted to be putatively functional SNPs. The risk associations with 16 SNPs around DUSP14 (rs1051849) and a previous reported melanoma locus MAFF/PLA2G6 (proxy SNP rs4608623) were replicated in the GenoMEL dataset (P < 0.01) but failed in the Australian dataset. Meta-analysis showed that rs1051849 in the 3' untranslated regions of DUSP14 was associated with a reduced risk of melanoma (odds ratio = 0.89, 95% confidence interval: 0.82-0.96, P = 0.003, false discovery rate = 0.056). Further genotype-phenotype correlation analysis using the 90 HapMap lymphoblastoid cell lines from Caucasians showed significant correlations between two SNPs (rs1051849 and rs4608623) and messenger RNA expression levels of DUSP14 and MAFF (P = 0.025 and P = 0.010, respectively). Gene-based tests also revealed significant SNPs were over-represented in MAFF, PLA2G6, DUSP14 and other 16 genes. Our results suggest that functional SNPs in MAPK pathways may contribute to CM risk. Further studies are warranted to validate our findings.
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Affiliation(s)
- Hongliang Liu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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14
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Wu CC, Shete S, Jo EJ, Xu Y, Lu EY, Chen WV, Amos CI. Whole-genome detection of disease-associated deletions or excess homozygosity in a case-control study of rheumatoid arthritis. Hum Mol Genet 2012; 22:1249-61. [PMID: 23223014 DOI: 10.1093/hmg/dds512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Unlike genome-wide association studies, few comprehensive studies of copy number variation's contribution to complex human disease susceptibility have been performed. Copy number variations are abundant in humans and represent one of the least well-studied classes of genetic variants; in addition, known rheumatoid arthritis susceptibility loci explain only a portion of familial clustering. Therefore, we performed a genome-wide study of association between deletion or excess homozygosity and rheumatoid arthritis using high-density 550 K SNP genotype data from a genome-wide association study. We used a genome-wide statistical method that we recently developed to test each contiguous SNP locus between 868 cases and 1194 controls to detect excess homozygosity or deletion variants that influence susceptibility. Our method is designed to detect statistically significant evidence of deletions or homozygosity at individual SNPs for SNP-by-SNP analyses and to combine the information among neighboring SNPs for cluster analyses. In addition to successfully detecting the known deletion variants on major histocompatibility complex, we identified 4.3 and 28 kb clusters on chromosomes 10p and 13q, respectively, which were significant at a Bonferroni-type-corrected 0.05 nominal significant level. Independently, we performed analyses using PennCNV, an algorithm for identifying and cataloging copy numbers for individuals based on a hidden Markov model, and identified cases and controls that had chromosomal segments with copy number <2. Using Fisher's exact test for comparing the numbers of cases and controls with copy number <2 per SNP, we identified 26 significant SNPs (protective; more controls than cases) aggregating on chromosome 14 with P-values <10(-8).
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Affiliation(s)
- Chih-Chieh Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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15
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Chen J, Pande M, Huang YJ, Wei C, Amos CI, Talseth-Palmer BA, Meldrum CJ, Chen WV, Gorlov IP, Lynch PM, Scott RJ, Frazier ML. Cell cycle-related genes as modifiers of age of onset of colorectal cancer in Lynch syndrome: a large-scale study in non-Hispanic white patients. Carcinogenesis 2012; 34:299-306. [PMID: 23125224 DOI: 10.1093/carcin/bgs344] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Heterogeneity in age of onset of colorectal cancer in individuals with mutations in DNA mismatch repair genes (Lynch syndrome) suggests the influence of other lifestyle and genetic modifiers. We hypothesized that genes regulating the cell cycle influence the observed heterogeneity as cell cycle-related genes respond to DNA damage by arresting the cell cycle to provide time for repair and induce transcription of genes that facilitate repair. We examined the association of 1456 single nucleotide polymorphisms (SNPs) in 128 cell cycle-related genes and 31 DNA repair-related genes in 485 non-Hispanic white participants with Lynch syndrome to determine whether there are SNPs associated with age of onset of colorectal cancer. Genotyping was performed on an Illumina GoldenGate platform, and data were analyzed using Kaplan-Meier survival analysis, Cox regression analysis and classification and regression tree (CART) methods. Ten SNPs were independently significant in a multivariable Cox proportional hazards regression model after correcting for multiple comparisons (P < 5 × 10(-4)). Furthermore, risk modeling using CART analysis defined combinations of genotypes for these SNPs with which subjects could be classified into low-risk, moderate-risk and high-risk groups that had median ages of colorectal cancer onset of 63, 50 and 42 years, respectively. The age-associated risk of colorectal cancer in the high-risk group was more than four times the risk in the low-risk group (hazard ratio = 4.67, 95% CI = 3.16-6.92). The additional genetic markers identified may help in refining risk groups for more tailored screening and follow-up of non-Hispanic white patients with Lynch syndrome.
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Affiliation(s)
- Jinyun Chen
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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16
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Amos CI, Schnell A, Chen WV, Elston RC. Model-free tests for genetic linkage. Curr Protoc Hum Genet 2012; Chapter 1:Unit1.8. [PMID: 23074068 DOI: 10.1002/0471142905.hg0108s75] [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] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This unit covers statistical methods of linkage analysis that do not require the assumption of a detailed genetic model, as is required for standard lod score analysis. The unit has been updated to include the latest methods in sib-pair analysis, including updates to using the software program SIBPAL as well as the relative-pair analysis software applications GENEHUNTER, GENEHUNTER PLUS, and Merlin.
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17
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Liu H, Wang LE, Liu Z, Chen WV, Amos CI, Lee JE, Iles MM, Law MH, Barrett JH, Montgomery GW, Taylor J, MacGregor S, Bishop JAN, Hayward NK, Bishop DT, Affleck P, Wei Q. Abstract LB-335: Associations of functional polymorphisms in genes involved in the MAPK signaling pathways and cutaneous melanoma risk. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-lb-335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Abstract
Cutaneous melanoma (CM) is the most aggressive form of skin cancers, and its incidence is increasing annually in Caucasian populations. Previous linkage studies have identified two high-penetrance genes that influence CM risk, including cyclin-dependent kinase inhibitor 2A (CDKN2A) and cyclin-dependent kinase 4 (CDK4). Recent genome-wide association studies (GWASs) on CM have successfully identified several low-penetrance loci on CM susceptibility. However, most GWASs have mainly focused on top significant single nucleotide polymorphisms (SNPs) that could reach the required genome-wide significance level, most of which did not have clear biological functions but were just surrogates for causal variants. To overcome these limitations in GWASs, several complementary approaches have been proposed recently, such as pathway-based analysis and integration analysis of association results with gene expression. These applications have successfully revealed several new cancer susceptibility genes and pathways. Thus, studying SNPs with moderate significance and putative functions in a specific pathway might be helpful to identify SNPs with a relative small effect size and provide additional insight into genetic mechanisms of cancer. Because MAPK pathways play critical roles in development and progression of CM, in this study, we reevaluated the associations between SNPs in 280 MAPK genes and melanoma risk in the discovery GWAS dataset for 1804 CM cases and 1026 cancer-free controls. We found that 34 SNPs with a significance level of 0.001. We further performed in silico prediction using SNPinfo and identified 11 SNPs with putative functions or having a high LD with functional SNPs, five of which were selected to be validated in two other GWAS datasets. A meta-analysis showed that two SNPs (rs1051849 in DUSP14 and rs4608623 near MAFF/PLA2G6) were associated with reduced CM risk (P = 0.0002 for rs1051849 and P = 0.00007 for rs4608623). Further correlation analysis of gene expression levels and SNP genotypes from 90 HapMap CEU cell lines revealed that these two SNPs had significant effects on mRNA expression of DUSP14 and MAFF, respectively (P = 0.025 for rs1051849 and P = 0.010 for rs4608623). We also performed gene-based tests using the hypergeometric method and the Versatile Gene-Based Test for Genome-wide Association (VEGAS) and found that significant SNPs were over-represented in 9 MAPK genes including DUSP14 and MAFF. Our results indicated that genetic variants in DUSP14 and MAFF might be associated with melanoma risk by influencing mRNA expression levels. Further studies are warranted to validate our findings.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-335. doi:1538-7445.AM2012-LB-335
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Affiliation(s)
- Hongliang Liu
- 1Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX
| | - Li-E Wang
- 1Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX
| | - Zhensheng Liu
- 1Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX
| | - Wei V Chen
- 2Department of Genetics, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Christopher I Amos
- 2Department of Genetics, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Jeffrey E Lee
- 3Department of Surgical Oncology, The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Mark M Iles
- 4Section of Epidemiology and Biostatistics, Cancer Research UK Clinical Centre, Leeds Institute of Molecular Medicine, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Matthew H Law
- 5Queensland Institute of Medical Research, Brisbane, Australia
| | - Jennifer H Barrett
- 4Section of Epidemiology and Biostatistics, Cancer Research UK Clinical Centre, Leeds Institute of Molecular Medicine, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Grant W Montgomery
- 6Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - John Taylor
- 4Section of Epidemiology and Biostatistics, Cancer Research UK Clinical Centre, Leeds Institute of Molecular Medicine, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Stuart MacGregor
- 6Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Julia A Newton Bishop
- 4Section of Epidemiology and Biostatistics, Cancer Research UK Clinical Centre, Leeds Institute of Molecular Medicine, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Nicholas K Hayward
- 6Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - D Timothy Bishop
- 4Section of Epidemiology and Biostatistics, Cancer Research UK Clinical Centre, Leeds Institute of Molecular Medicine, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Paul Affleck
- 6Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Qingyi Wei
- 7Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX
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18
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Amos CI, Wang LE, Lee JE, Gershenwald JE, Chen WV, Fang S, Kosoy R, Zhang M, Qureshi AA, Vattathil S, Schacherer CW, Gardner JM, Wang Y, Bishop DT, Barrett JH, MacGregor S, Hayward NK, Martin NG, Duffy DL, Mann GJ, Cust A, Hopper J, Brown KM, Grimm EA, Xu Y, Han Y, Jing K, McHugh C, Laurie CC, Doheny KF, Pugh EW, Seldin MF, Han J, Wei Q. Genome-wide association study identifies novel loci predisposing to cutaneous melanoma. Hum Mol Genet 2011; 20:5012-23. [PMID: 21926416 DOI: 10.1093/hmg/ddr415] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We performed a multistage genome-wide association study of melanoma. In a discovery cohort of 1804 melanoma cases and 1026 controls, we identified loci at chromosomes 15q13.1 (HERC2/OCA2 region) and 16q24.3 (MC1R) regions that reached genome-wide significance within this study and also found strong evidence for genetic effects on susceptibility to melanoma from markers on chromosome 9p21.3 in the p16/ARF region and on chromosome 1q21.3 (ARNT/LASS2/ANXA9 region). The most significant single-nucleotide polymorphisms (SNPs) in the 15q13.1 locus (rs1129038 and rs12913832) lie within a genomic region that has profound effects on eye and skin color; notably, 50% of variability in eye color is associated with variation in the SNP rs12913832. Because eye and skin colors vary across European populations, we further evaluated the associations of the significant SNPs after carefully adjusting for European substructure. We also evaluated the top 10 most significant SNPs by using data from three other genome-wide scans. Additional in silico data provided replication of the findings from the most significant region on chromosome 1q21.3 rs7412746 (P = 6 × 10(-10)). Together, these data identified several candidate genes for additional studies to identify causal variants predisposing to increased risk for developing melanoma.
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Affiliation(s)
- Christopher I Amos
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Pande M, Spitz MR, Wu X, Gorlov IP, Chen WV, Amos CI. Novel genetic variants in the chromosome 5p15.33 region associate with lung cancer risk. Carcinogenesis 2011; 32:1493-9. [PMID: 21771723 DOI: 10.1093/carcin/bgr136] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Chromosome 5p15.33 has been identified by genome-wide association studies as one of the regions that associate with lung cancer risk. A few single-nucleotide polymorphisms (SNPs) in the telomerase reverse transcriptase (TERT) and cleft lip and palate transmembrane 1-like (CLPTM1L) genes located in this region have shown consistent associations. We performed dense genotyping of SNPs in this region to refine the previously reported association signals for lung cancer risk. Two hundred and fifteen SNPs were genotyped on an Illumina iSelect panel, in a hospital-based case-control study of 1681 lung cancer cases and 1235 unaffected controls. Association was tested using unconditional logistic regression, while adjusting for age, sex and pack-years smoked. Furthermore, since many of the SNPs were in linkage disequilibrium (LD), haplotype blocks were constructed, from which tagging SNPs at an r(2) threshold of ≥0.95 were included in a stepwise forward selection logistic regression model. Of the 215 SNPs, 69 were significant at P < 0.05 in univariate analysis; of these, 35 SNPs meeting the r(2) threshold were included in the multiple logistic regression model. Two SNPs, rs370348 (odds ratio = 0.76, P = 1.6 × 10(-6)) and rs4975538 (odds ratio = 1.18, P = 0.005), significantly associated with risk in the overall sample. Among ever smokers, rs4975615 (odds ratio = 0.75, P = 1.2 × 10(-4)) and rs4975538 (odds ratio = 1.26, P = 0.002) were significant, whereas among never-smokers, rs451360 (odds ratio = 0.62, P = 7.6 × 10(-5)) was significant. We refined the consistent association signal in this region, allowing for the considerable LD between SNPs and identified four novel SNPs that were independently and significantly associated with lung cancer risk. Results of these analyses strongly suggest effects on risk from several loci in the TERT/CLPTM1L region.
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Affiliation(s)
- Mala Pande
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston,TX 77030, USA
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20
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Yu H, Zhao H, Wang LE, Han Y, Chen WV, Amos CI, Rafnar T, Sulem P, Stefansson K, Landi MT, Caporaso N, Albanes D, Thun M, McKay JD, Brennan P, Wang Y, Houlston RS, Spitz MR, Wei Q. An analysis of single nucleotide polymorphisms of 125 DNA repair genes in the Texas genome-wide association study of lung cancer with a replication for the XRCC4 SNPs. DNA Repair (Amst) 2011; 10:398-407. [PMID: 21296624 DOI: 10.1016/j.dnarep.2011.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 12/11/2010] [Accepted: 01/09/2011] [Indexed: 10/18/2022]
Abstract
DNA repair genes are important for maintaining genomic stability and limiting carcinogenesis. We analyzed all single nucleotide polymorphisms (SNPs) of 125 DNA repair genes covered by the Illumina HumanHap300 (v1.1) BeadChips in a previously conducted genome-wide association study (GWAS) of 1154 lung cancer cases and 1137 controls and replicated the top-hits of XRCC4 SNPs in an independent set of 597 cases and 611 controls in Texas populations. We found that six of 20 XRCC4 SNPs were associated with a decreased risk of lung cancer with a P-value of 0.01 or lower in the discovery dataset, of which the most significant SNP was rs10040363 (P for allelic test=4.89 x 10⁻⁴). Moreover, the data in this region allowed us to impute a potentially functional SNP rs2075685 (imputed P for allelic test=1.3 x 10⁻³). A luciferase reporter assay demonstrated that the rs2075685G>T change in the XRCC4 promoter increased expression of the gene. In the replication study of rs10040363, rs1478486, rs9293329, and rs2075685, however, only rs10040363 achieved a borderline association with a decreased risk of lung cancer in a dominant model (adjusted OR=0.80, 95% CI=0.62-1.03 and P=0.079). In the final combined analysis of both the Texas GWAS discovery and replication datasets, the strength of the association was increased for rs10040363 (adjusted OR=0.77, 95% CI=0.66-0.89, P(dominant)=5 x 10⁻⁴ and P for trend=5 x 10⁻⁴) and rs1478486 (adjusted OR=0.82, 95% CI=0.71-0.94, P(dominant)=6 x 10⁻³ and P for trend=3.5 x 10⁻³). Finally, we conducted a meta-analysis of these XRCC4 SNPs with available data from published GWA studies of lung cancer with a total of 12,312 cases and 47,921 controls, in which none of these XRCC4 SNPs was associated with lung cancer risk. It appeared that rs2075685, although associated with increased expression of a reporter gene and lung cancer risk in the Texas populations, did not have an effect on lung cancer risk in other populations. This study underscores the importance of replication using published data in larger populations.
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Affiliation(s)
- Hongping Yu
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
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21
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Wei S, Niu J, Zhao H, Liu Z, Wang LE, Han Y, Chen WV, Amos CI, Rafnar T, Sulem P, Stefansson K, Landi MT, Caporaso NE, Albanes D, Thun MJ, McKay JD, Brennan P, Wang Y, Houlston RS, Spitz MR, Wei Q. Association of a novel functional promoter variant (rs2075533 C>T) in the apoptosis gene TNFSF8 with risk of lung cancer--a finding from Texas lung cancer genome-wide association study. Carcinogenesis 2011; 32:507-15. [PMID: 21292647 DOI: 10.1093/carcin/bgr014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Published genome-wide association studies (GWASs) have identified few variants in the known biological pathways involved in lung cancer etiology. To mine the possibly hidden causal single nucleotide polymorphisms (SNPs), we explored all SNPs in the extrinsic apoptosis pathway from our published GWAS dataset for 1154 lung cancer cases and 1137 cancer-free controls. In an initial association analysis of 611 tagSNPs in 41 apoptosis-related genes, we identified only 10 tagSNPs associated with lung cancer risk with a P value<10(-2), including four tagSNPs in DAPK1 and three tagSNPs in TNFSF8. Unlike DAPK1 SNPs, TNFSF8 rs2181033 tagged other four predicted functional but untyped SNPs (rs776576, rs776577, rs31813148 and rs2075533) in the promoter region. Therefore, we further tested binding affinity of these four SNPs by performing the electrophoretic mobility shift assay. We found that only rs2075533T allele modified levels of nuclear proteins bound to DNA, leading to significantly decreased expression of luciferase reporter constructs by 5- to -10-fold in H1299, HeLa and HCT116 cell lines compared with the C allele. We also performed a replication study of the untyped rs2075533 in an independent Texas population but did not confirm the protective effect. We further performed a mini meta-analysis for SNPs of TNFSF8 obtained from other four published lung cancer GWASs with 12 214 cases and 47 721 controls, and we found that only rs3181366 (r2=0.69 with the untyped rs2075533) was associated to lung cancer risk (P=0.008). Our findings suggest a possible role of novel TNFSF8 variants in susceptibility to lung cancer.
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Affiliation(s)
- Sheng Wei
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA
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Petukhova L, Duvic M, Hordinsky M, Norris D, Price V, Shimomura Y, Kim H, Singh P, Lee A, Chen WV, Meyer KC, Paus R, Jahoda CAB, Amos CI, Gregersen PK, Christiano AM. Genome-wide association study in alopecia areata implicates both innate and adaptive immunity. Nature 2010; 466:113-7. [PMID: 20596022 DOI: 10.1038/nature09114] [Citation(s) in RCA: 524] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 04/22/2010] [Indexed: 12/18/2022]
Abstract
Alopecia areata (AA) is among the most highly prevalent human autoimmune diseases, leading to disfiguring hair loss due to the collapse of immune privilege of the hair follicle and subsequent autoimmune attack. The genetic basis of AA is largely unknown. We undertook a genome-wide association study (GWAS) in a sample of 1,054 cases and 3,278 controls and identified 139 single nucleotide polymorphisms that are significantly associated with AA (P <or= 5 x 10(-7)). Here we show an association with genomic regions containing several genes controlling the activation and proliferation of regulatory T cells (T(reg) cells), cytotoxic T lymphocyte-associated antigen 4 (CTLA4), interleukin (IL)-2/IL-21, IL-2 receptor A (IL-2RA; CD25) and Eos (also known as Ikaros family zinc finger 4; IKZF4), as well as the human leukocyte antigen (HLA) region. We also find association evidence for regions containing genes expressed in the hair follicle itself (PRDX5 and STX17). A region of strong association resides within the ULBP (cytomegalovirus UL16-binding protein) gene cluster on chromosome 6q25.1, encoding activating ligands of the natural killer cell receptor NKG2D that have not previously been implicated in an autoimmune disease. By probing the role of ULBP3 in disease pathogenesis, we also show that its expression in lesional scalp from patients with AA is markedly upregulated in the hair follicle dermal sheath during active disease. This study provides evidence for the involvement of both innate and acquired immunity in the pathogenesis of AA. We have defined the genetic underpinnings of AA, placing it within the context of shared pathways among autoimmune diseases, and implicating a novel disease mechanism, the upregulation of ULBP ligands, in triggering autoimmunity.
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Affiliation(s)
- Lynn Petukhova
- Department of Dermatology, Columbia University, New York, New York 10032, USA
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23
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Wu CC, Shete S, Chen WV, Peng B, Lee AT, Ma J, Gregersen PK, Amos CI. Detection of disease-associated deletions in case-control studies using SNP genotypes with application to rheumatoid arthritis. Hum Genet 2009; 126:303-15. [PMID: 19415332 DOI: 10.1007/s00439-009-0672-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Accepted: 04/12/2009] [Indexed: 10/20/2022]
Abstract
Genomic deletions have long been known to play a causative role in microdeletion syndromes. Recent whole-genome genetic studies have shown that deletions can increase the risk for several psychiatric disorders, suggesting that genomic deletions play an important role in the genetic basis of complex traits. However, the association between genomic deletions and common, complex diseases has not yet been systematically investigated in gene mapping studies. Likelihood-based statistical methods for identifying disease-associated deletions have recently been developed for familial studies of parent-offspring trios. The purpose of this study is to develop statistical approaches for detecting genomic deletions associated with complex disease in case-control studies. Our methods are designed to be used with dense single nucleotide polymorphism (SNP) genotypes to detect deletions in large-scale or whole-genome genetic studies. As more and more SNP genotype data for genome-wide association studies become available, development of sophisticated statistical approaches will be needed that use these data. Our proposed statistical methods are designed to be used in SNP-by-SNP analyses and in cluster analyses based on combined evidence from multiple SNPs. We found that these methods are useful for detecting disease-associated deletions and are robust in the presence of linkage disequilibrium using simulated SNP data sets. Furthermore, we applied the proposed statistical methods to SNP genotype data of chromosome 6p for 868 rheumatoid arthritis patients and 1,197 controls from the North American Rheumatoid Arthritis Consortium. We detected disease-associated deletions within the region of human leukocyte antigen in which genomic deletions were previously discovered in rheumatoid arthritis patients.
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Affiliation(s)
- Chih-Chieh Wu
- Unit 1340, Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA.
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24
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Chen WV, Amos CI, Etzel CJ, Shete S, Gregersen PK. Comparison of genome-wide single-nucleotide polymorphism linkage analyses in Caucasian and Hispanic NARAC families. BMC Proc 2007; 1 Suppl 1:S97. [PMID: 18466601 PMCID: PMC2367594 DOI: 10.1186/1753-6561-1-s1-s97] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [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: 11/10/2022] Open
Abstract
We performed linkage analysis on families with rheumatoid arthritis, stratifying by ethnic origin. We compared results using either Kong and Cox nonparametric LOD scores or MOD score analysis using the software GeneHunter MODSCORE. We first applied SNPLINK to remove markers showing excess linkage disequilibrium from the SNPs in the Illumina IV SNP Linkage panel. In this analysis there were 659 self-reported Caucasian families and 29 self-reported Hispanic families in the NARAC collection. Chromosome 19 yielded MOD scores > 3.00 in the Hispanic group, while chromosomes 2, 6, 7, 11, and XY had MOD scores > 3.00 in the Caucasian group. We performed simulation studies to evaluate the empirical distribution of the MOD score for autosomal loci separately in Hispanics and Caucasians. Results showed genome-wide significant evidence for linkage in Caucasians for chromosomes 2q and 6p, but no significant evidence for any linkages in the Hispanics, including little evidence for linkage to chromosome 6p in this group. An examination of the difference of phenotypes in two ethnic groups suggested significantly earlier mean age of onset, higher percentage of anti-cyclic citrullinated peptide positive people, and lower percentage of affected people carrying shared epitopes in Hispanics than those in Caucasians. A larger sample size of the Hispanic group is needed to identify linkage regions.
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Affiliation(s)
- Wei V Chen
- Department of Epidemiology, U.T. M.D. Anderson Cancer Center, Houston, Texas 77030, USA.
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25
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Ghosh S, Babron MC, Amos CI, Briollais L, Chen P, Chen WV, Chiu WF, Drigalenko E, Etzel CJ, Hamshere ML, Holmans PA, Margaritte-Jeannin P, Lebrec JJP, Lin S, Lin WY, Mandhyan DD, Nishchenko I, Schaid DJ, Seguardo R, Shete S, Taylor K, Tayo BO, Wan S, Wei LY, Wu CO, Yang XR. Linkage analyses of rheumatoid arthritis and related quantitative phenotypes: the GAW15 experience. Genet Epidemiol 2007; 31 Suppl 1:S86-95. [PMID: 18046767 DOI: 10.1002/gepi.20284] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The group that formed on the theme of linkage analyses of rheumatoid arthritis RA and related phenotypes (Group 10) in the Genetic Analysis Workshop 15 comprised 18 sets of investigators. Two data sets were available: one was a real set provided by the North American Rheumatoid Arthritis Consortium and collaborators in Canada, France (European Consortium Of Rheumatoid Arthritis Families) and the UK; the other was a simulated data set modelled after the real data set. Whereas a majority of the investigators analyzed the RA affection status as a binary phenotype, a few contributions considered data on correlated quantitative traits such as anti-cyclic citrullinated peptide and rheumatoid factor-immunoglobulin M. The different investigators applied a wide spectrum of linkage methods. As expected, most methods could identify the human leukocyfeantigen region on chromosome 6 as a major genetic factor for RA. In addition, some novel chromosomal regions provided significant evidence of linkage in multiple contributions in the group. In this report, we discuss the different strategies explored by the different investigators with the common goal of improving the power to detect linkage.
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Affiliation(s)
- Saurabh Ghosh
- Human Genetics Unit, Indian Statistical Institute, 203 B.T. Road, Kolkata 700-108, India.
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Plenge RM, Seielstad M, Padyukov L, Lee AT, Remmers EF, Ding B, Liew A, Khalili H, Chandrasekaran A, Davies LR, Li W, Tan AK, Bonnard C, Ong RT, Thalamuthu A, Pettersson S, Liu C, Tian C, Chen WV, Carulli JP, Beckman EM, Altshuler D, Alfredsson L, Criswell LA, Amos CI, Seldin MF, Kastner DL, Klareskog L, Gregersen PK. TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study. N Engl J Med 2007; 357:1199-209. [PMID: 17804836 PMCID: PMC2636867 DOI: 10.1056/nejmoa073491] [Citation(s) in RCA: 641] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Rheumatoid arthritis has a complex mode of inheritance. Although HLA-DRB1 and PTPN22 are well-established susceptibility loci, other genes that confer a modest level of risk have been identified recently. We carried out a genomewide association analysis to identify additional genetic loci associated with an increased risk of rheumatoid arthritis. METHODS We genotyped 317,503 single-nucleotide polymorphisms (SNPs) in a combined case-control study of 1522 case subjects with rheumatoid arthritis and 1850 matched control subjects. The patients were seropositive for autoantibodies against cyclic citrullinated peptide (CCP). We obtained samples from two data sets, the North American Rheumatoid Arthritis Consortium (NARAC) and the Swedish Epidemiological Investigation of Rheumatoid Arthritis (EIRA). Results from NARAC and EIRA for 297,086 SNPs that passed quality-control filters were combined with the use of Cochran-Mantel-Haenszel stratified analysis. SNPs showing a significant association with disease (P<1x10(-8)) were genotyped in an independent set of case subjects with anti-CCP-positive rheumatoid arthritis (485 from NARAC and 512 from EIRA) and in control subjects (1282 from NARAC and 495 from EIRA). RESULTS We observed associations between disease and variants in the major-histocompatibility-complex locus, in PTPN22, and in a SNP (rs3761847) on chromosome 9 for all samples tested, the latter with an odds ratio of 1.32 (95% confidence interval, 1.23 to 1.42; P=4x10(-14)). The SNP is in linkage disequilibrium with two genes relevant to chronic inflammation: TRAF1 (encoding tumor necrosis factor receptor-associated factor 1) and C5 (encoding complement component 5). CONCLUSIONS A common genetic variant at the TRAF1-C5 locus on chromosome 9 is associated with an increased risk of anti-CCP-positive rheumatoid arthritis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Peter K. Gregersen
- The authors' affiliations are listed in the Appendix. Address reprint requests to Dr. Gregersen at the Feinstein Institute for Medical Research, 350 Community Dr., Manhasset, NY 11030, or at
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Remmers EF, Plenge RM, Lee AT, Graham RR, Hom G, Behrens TW, de Bakker PIW, Le JM, Lee HS, Batliwalla F, Li W, Masters SL, Booty MG, Carulli JP, Padyukov L, Alfredsson L, Klareskog L, Chen WV, Amos CI, Criswell LA, Seldin MF, Kastner DL, Gregersen PK. STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. N Engl J Med 2007; 357:977-86. [PMID: 17804842 PMCID: PMC2630215 DOI: 10.1056/nejmoa073003] [Citation(s) in RCA: 747] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND Rheumatoid arthritis is a chronic inflammatory disease with a substantial genetic component. Susceptibility to disease has been linked with a region on chromosome 2q. METHODS We tested single-nucleotide polymorphisms (SNPs) in and around 13 candidate genes within the previously linked chromosome 2q region for association with rheumatoid arthritis. We then performed fine mapping of the STAT1-STAT4 region in a total of 1620 case patients with established rheumatoid arthritis and 2635 controls, all from North America. Implicated SNPs were further tested in an independent case-control series of 1529 patients with early rheumatoid arthritis and 881 controls, all from Sweden, and in a total of 1039 case patients and 1248 controls from three series of patients with systemic lupus erythematosus. RESULTS A SNP haplotype in the third intron of STAT4 was associated with susceptibility to both rheumatoid arthritis and systemic lupus erythematosus. The minor alleles of the haplotype-defining SNPs were present in 27% of chromosomes of patients with established rheumatoid arthritis, as compared with 22% of those of controls (for the SNP rs7574865, P=2.81x10(-7); odds ratio for having the risk allele in chromosomes of patients vs. those of controls, 1.32). The association was replicated in Swedish patients with recent-onset rheumatoid arthritis (P=0.02) and matched controls. The haplotype marked by rs7574865 was strongly associated with lupus, being present on 31% of chromosomes of case patients and 22% of those of controls (P=1.87x10(-9); odds ratio for having the risk allele in chromosomes of patients vs. those of controls, 1.55). Homozygosity of the risk allele, as compared with absence of the allele, was associated with a more than doubled risk for lupus and a 60% increased risk for rheumatoid arthritis. CONCLUSIONS A haplotype of STAT4 is associated with increased risk for both rheumatoid arthritis and systemic lupus erythematosus, suggesting a shared pathway for these illnesses.
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Affiliation(s)
- Elaine F Remmers
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, USA
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Criswell LA, Chen WV, Jawaheer D, Lum RF, Wener MH, Gu X, Gregersen PK, Amos CI. Dissecting the heterogeneity of rheumatoid arthritis through linkage analysis of quantitative traits. ACTA ACUST UNITED AC 2007; 56:58-68. [PMID: 17195208 DOI: 10.1002/art.22325] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To dissect the heterogeneity of rheumatoid arthritis (RA) through linkage analysis of quantitative traits, specifically, IgM rheumatoid factor (IgM-RF) and anti-cyclic citrullinated peptide (anti-CCP) autoantibody titers. METHODS Subjects, 1,002 RA patients from 491 multiplex families recruited by the North American RA Consortium, were typed for 379 microsatellite markers. Anti-CCP titers were determined based on a second-generation enzyme-linked immunosorbent assay, and IgM-RF levels were quantified by immunonephelometry. We used the Merlin statistical package to perform nonparametric quantitative trait linkage analysis. RESULTS For each of the quantitative traits, evidence of linkage, with logarithm of odds (LOD) scores of >1.0, was found in 9 regions. For both traits, the strongest evidence of linkage was for marker D6S1629 on chromosome 6p (LOD 14.02 for anti-CCP and LOD 12.09 for RF). Six other regions with LOD scores of >1.0 overlapped between the 2 traits, on chromosomes 1p21.1, 5q15, 8p23.1, 16p12.1, 16q23.1, and 18q21.31. Evidence of linkage to anti-CCP titer but not to RF titer was found in 2 regions (chromosomes 9p21.3 and 10q21.1), and evidence of linkage to RF titer but not to anti-CCP titer was found in 2 regions (chromosomes 5p15.2 and 1q42.3). Several covariates were significantly associated with 1 or both traits, and linkage analysis exploring the covariate effects revealed striking effects of sex in modulating linkage signals for several chromosomal regions. For example, sex had a striking impact on the linkage results for both quantitative traits on chromosome 6p (P = 0.0007 for anti-CCP titer and P = 0.0012 for RF titer), suggesting a sex-HLA region interaction. CONCLUSION Analysis of quantitative components of RA is a promising approach for dissecting the genetic heterogeneity of this complex disorder. These results highlight the potential importance of sex or other covariates that may modulate some of the genetic effects that influence the risk of specific disease manifestations.
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Amos CI, Chen WV, Lee A, Li W, Kern M, Lundsten R, Batliwalla F, Wener M, Remmers E, Kastner DA, Criswell LA, Seldin MF, Gregersen PK. High-density SNP analysis of 642 Caucasian families with rheumatoid arthritis identifies two new linkage regions on 11p12 and 2q33. Genes Immun 2006; 7:277-86. [PMID: 16691188 DOI: 10.1038/sj.gene.6364295] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We have completed a genome wide linkage scan using >5700 informative single-nucleotide polymorphism (SNP) markers (Illumina IV SNP linkage panel) in 642 Caucasian families containing affected sibling pairs with rheumatoid arthritis (RA), ascertained by the North American Rheumatoid Arthritis Consortium. The results show striking new evidence of linkage at chromosomes 2q33 and 11p12 with logarithm of odds (LOD) scores of 3.52 and 3.09, respectively. In addition to a strong and broad linkage interval surrounding the major histocompatibility complex (LOD>16), regions with LOD>2.5 were observed on chromosomes 5 and 10. Additional linkage evidence (LOD scores between 1.46 and 2.35) was also observed on chromosomes 4, 7, 12, 16 and 18. This new evidence for multiple regions of genetic linkage is partly explained by the significantly increased information content of the Illumina IV SNP linkage panel (75.6%) compared with a standard microsatellite linkage panel utilized previously (mean 52.6%). Stratified analyses according to whether or not the sibling pair members showed elevated anticyclic citrullinated peptide titers indicates significant variation in evidence for linkage among strata on chromosomes 4, 5, 6 and 7. Overall, these new linkage data should reinvigorate efforts to utilize positional information to identify susceptibility genes for RA.
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Affiliation(s)
- C I Amos
- Department of Epidemiology, University of Texas, MD Anderson Cancer Center, Houston, USA
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Abstract
In humans, spontaneous DZ twinning is known to have a genetic basis. A prior investigation in the Flemish and Dutch population showed that the phenotype of 'having DZ twins' was consistent with an autosomal monogenic dominant model, with a gene frequency of 3.5% and a female-specific lifetime penetrance of 10%. Recessive, X-linked, polygenic and sporadic models were rejected. This study reports on a genome-wide scan of 14 Flemish families containing 57 mothers of spontaneous DZ twins. Two-point linkage analysis using the autosomal dominant model showed nine chromosomal regions with a LOD score around 1. After multipoint linkage analysis, including heterogeneity, three chromosomes continued to give high LOD scores. These regions were further haplotyped with additional markers at 1 cM distance. The multipoint analysis was not in favour of linkage of the DZ twinning trait in most candidate genes and other regions (LOD score < -2) under the genetic model of autosomal dominance. To further evaluate the evidence for linkage given some uncertainty about the correct mode of inheritance of twinning susceptibility other models of inheritance were tested. Results of this analysis showed all models gave highest LOD scores under dominant models. If heterogeneity among the families is taken into account, the peaks that were observed on chromosome 2, 7 and 18 could well contain a potential gene contributing to DZ twinning. These results give suggestive evidence that the mode of inheritance of DZ twinning is probably more complex than was originally expected.
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Affiliation(s)
- Catherine Derom
- Department of Human Genetics, University Hospital Gasthuisberg, Katholieke Universiteit Leuven, Leuven, Belgium.
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Etzel CJ, Chen WV, Shepard N, Jawaheer D, Cornelis F, Seldin MF, Gregersen PK, Amos CI. Genome-wide meta-analysis for rheumatoid arthritis. Hum Genet 2006; 119:634-41. [PMID: 16612613 DOI: 10.1007/s00439-006-0171-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2005] [Accepted: 03/14/2006] [Indexed: 01/20/2023]
Abstract
Meta-analysis is being increasingly used as a tool for integrating data from different studies of complex phenotypes, because the power of any one study to identify causal loci is limited. We applied a novel meta-analytical approach (Loesgen et al. in Genet Epidemiol 21(Suppl 1):S142-S147, 2001) in compiling results from four studies of rheumatoid arthritis in Caucasians including two studies from NARAC (Jawaheer et al. in Am J Hum Genet 68:927-936, 2001; Jawaheer et al. in Arthritis Rheum 48:906-916, 2003), one study from the UK (MacKay et al. in Arthritis Rheum 46:632-639, 2001) and one from France (Cornelis et al. in Proc Natl Acad Sci USA 95:10746-10750, 1998). For each study, we obtained NPL scores by performing interval mapping (2 cM intervals) using GeneHunter2 (Kruglyak et al. in Am J Hum Genet 58:1347-1363, 1996; Markianos et al. in Am J Hum Genet 68:963-977, 2001). The marker maps differed among the three consortium groups, therefore, the marker maps were aligned after the interval mapping was completed and the NPL scores that were within 1 cM of each other were combined using the method of Loesgen et al. (Genet Epidemiol 21(Suppl 1):S142-S147, 2001) by calculating the weighted average of the NPL score. This approach avoids some problems in analysis encountered by using GeneHunter2 when some markers in the sample are not genotyped. This procedure provided marginal evidence (P<0.05) of linkage on chromosome 1, 2, 5 and 18, strong evidence (P<0.01) on chromosomes 8 and 16, and overwhelming evidence in the HLA region of chromosome 6.
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Affiliation(s)
- Carol J Etzel
- Department of Epidemiology, UT MD Anderson Cancer Center, 1155 Pressler Street - Unit 1340, Houston, TX 77030, USA.
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Jawaheer D, Seldin MF, Amos CI, Chen WV, Shigeta R, Etzel C, Damle A, Xiao X, Chen D, Lum RF, Monteiro J, Kern M, Criswell LA, Albani S, Nelson JL, Clegg DO, Pope R, Schroeder HW, Bridges SL, Pisetsky DS, Ward R, Kastner DL, Wilder RL, Pincus T, Callahan LF, Flemming D, Wener MH, Gregersen PK. Screening the genome for rheumatoid arthritis susceptibility genes: a replication study and combined analysis of 512 multicase families. Arthritis Rheum 2003; 48:906-16. [PMID: 12687532 DOI: 10.1002/art.10989] [Citation(s) in RCA: 195] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE A number of non-HLA loci that have shown evidence (P < 0.05) for linkage with rheumatoid arthritis (RA) have been previously identified. The present study attempts to confirm these findings. METHODS We performed a second genome-wide screen of 256 new multicase RA families recruited from across the United States by the North American Rheumatoid Arthritis Consortium. Affected sibling pair analysis on the new data set was performed using SIBPAL. We subsequently combined our first and second data sets in an attempt to enhance the evidence for linkages in a larger sample size. We also evaluated the impact of covariates on the support for linkage, using LODPAL. RESULTS Evidence of linkage at 1p13 (D1S1631), 6p21.3 (the HLA complex), and 18q21 (D18S858) (P < 0.05) was replicated in this independent data set. In addition, there was new evidence for linkage at 9p22 (D9S1121 [P = 0.001]) and 10q21 (D10S1221 [P = 0.0002] and D10S1225 [P = 0.0038]) in the current data set. The combined analysis of both data sets (512 families) showed evidence for linkage at the level of P < 0.005 at 1p13 (D1S1631), 1q43 (D1S235), 6q21 (D6S2410), 10q21 (D10S1221), 12q12 (D12S398), 17p13 (D17S1298), and 18q21 (D18S858). Linkage at HLA was also confirmed (P < 5 x 10(-12)). Inclusion of DRB1*04 as a covariate significantly increased the probability of linkage on chromosome 6. In addition, some linkages on chromosome 1 showed improved significance when modeling DRB1*04 or rheumatoid factor positivity as covariates. CONCLUSION These results provide a rational basis for pursuing high-density linkage and association studies of RA in several regions outside of the HLA region, particularly on chromosomes 1p, 1q, and 18q.
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Affiliation(s)
- Damini Jawaheer
- Center for Genomics and Human Genetics, Manhasset, New York 11030, USA
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Chen WV, Fielding Hejtmancik J, Piatigorsky J, Duncan MK. The mouse beta B1-crystallin promoter: strict regulation of lens fiber cell specificity. Biochim Biophys Acta 2001; 1519:30-8. [PMID: 11406268 DOI: 10.1016/s0167-4781(01)00201-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Previous studies have shown that the chicken beta B1-crystallin promoter (-434/+30) contains all of the signals necessary to specifically direct high level expression of heterologous genes to the lens fiber cells of mice. In the present study, the mouse beta B1-crystallin gene was cloned, and its regulation was investigated to further elucidate the mechanisms controlling lens fiber cell-specific gene expression. Phylogenetic footprinting analysis of the 5' flanking sequence from the mouse, rat, human and chicken beta B1-crystallin genes identified several known and putative functional cis elements including the PL2 element which is required for lens-specific expression of the chicken beta B1 promoter. Surprisingly, however, all six mouse beta B1-crystallin/CAT constructs tested (-1493/+44, -1493/+30, -870/+30, -250/+30, -135/+30 and -98/+30) were inactive in three different mammalian lens-derived cell lines while only the -870/+30 and -98/+30 constructs were active in chicken primary patched lens epithelial cells. In contrast, the chicken beta B1-crystallin promoter (-434/+30) was transcriptionally active in all lens-derived cells tested. Transgenic mice harboring a mouse beta B1-crystallin -1493/+44 CAT construct did express the transgene specifically in lens fiber cells, however, at lower levels than that previously reported for a chicken -434/+30 CAT construct. These data suggest that, as in other crystallin genes, the regulatory signals controlling lens fiber cell-specific expression are conserved between chicken and mouse. However, the inability of the mouse beta B1-crystallin promoter to function in mammalian lens-derived cultured cells implies that this gene has acquired additional cis-regulatory elements to ensure lens fiber cell specificity.
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Affiliation(s)
- W V Chen
- Department of Biological Sciences, University of Delaware, Newark, 19716, USA
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Jawaheer D, Seldin MF, Amos CI, Chen WV, Shigeta R, Monteiro J, Kern M, Criswell LA, Albani S, Nelson JL, Clegg DO, Pope R, Schroeder Jr. HW, Bridges Jr. SL, Pisetsky DS, Ward R, Kastner DL, Wilder RL, Pincus T, Callahan LF, Flemming D, Wener MH, Gregersen PK. A genomewide screen in multiplex rheumatoid arthritis families suggests genetic overlap with other autoimmune diseases. Am J Hum Genet 2001; 68:927-36. [PMID: 11254450 PMCID: PMC1275647 DOI: 10.1086/319518] [Citation(s) in RCA: 286] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2000] [Accepted: 02/13/2001] [Indexed: 11/03/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune/inflammatory disorder with a complex genetic component. We report the first major genomewide screen of multiplex families with RA gathered in the United States. The North American Rheumatoid Arthritis Consortium, using well-defined clinical criteria, has collected 257 families containing 301 affected sibling pairs with RA. A genome screen for allele sharing was performed, using 379 microsatellite markers. A nonparametric analysis using SIBPAL confirmed linkage of the HLA locus to RA (P < .00005), with lambdaHLA = 1.79. However, the analysis also revealed a number of non-HLA loci on chromosomes 1 (D1S235), 4 (D4S1647), 12 (D12S373), 16 (D16S403), and 17 (D17S1301), with evidence for linkage at a significance level of P<.005. Analysis of X-linked markers using the MLOD method from ASPEX also suggests linkage to the telomeric marker DXS6807. Stratifying the families into white or seropositive subgroups revealed some additional markers that showed improvement in significance over the full data set. Several of the regions that showed evidence for nominal significance (P < .05) in our data set had previously been implicated in RA (D16S516 and D17S1301) or in other diseases of an autoimmune nature, including systemic lupus erythematosus (D1S235), inflammatory bowel disease (D4S1647, D5S1462, and D16S516), multiple sclerosis (D12S1052), and ankylosing spondylitis (D16S516). Therefore, genes in the HLA complex play a major role in RA susceptibility, but several other regions also contribute significantly to overall genetic risk.
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Affiliation(s)
- Damini Jawaheer
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Michael F. Seldin
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Christopher I. Amos
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Wei V. Chen
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Russell Shigeta
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Joanita Monteiro
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Marlene Kern
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Lindsey A. Criswell
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Salvatore Albani
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - J. Lee Nelson
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Daniel O. Clegg
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Richard Pope
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Harry W. Schroeder Jr.
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - S. Louis Bridges Jr.
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - David S. Pisetsky
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Ryk Ward
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Daniel L. Kastner
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Ronald L. Wilder
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Theodore Pincus
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Leigh F. Callahan
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Donald Flemming
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Mark H. Wener
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
| | - Peter K. Gregersen
- Division of Biology and Human Genetics, North Shore University Hospital, Manhasset, NY†; Department of Biological Chemistry, University of California at Davis, Davis, CA†; Departments of Epidemiology and Biomathematics, University of Texas M. D. Anderson Cancer Center, Houston; Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco†; Center for Pediatric Rheumatology, University of California at San Diego, La Jolla, CA†; Program in Immunogenetics, Fred Hutchinson Cancer Research Center,† and Department of Laboratory Medicine, University of Washington School of Medicine, Seattle; Department of Medicine, University of Utah, Salt Lake City†; Department of Medicine, Northwestern University Medical School, Chicago†; Departments of Medicine and Microbiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL†; Medical Research Service, Durham VA Hospital, Division of Rheumatology, Allergy, and Clinical Immunology, Duke University Medical Center, Durham, NC†; Institute of Biological Anthropology, University of Oxford, Oxford; Arthritis and Rheumatism Branch, National Institutes of Health/NIAMS,† and CDR, MC, USN, Department of Radiology, National Naval Medical Center, Bethesda; Department of Medicine, Vanderbilt University, Nashville†; and Department of Orthopedics and Medicine, Thurston Arthritis Research Center, University of North Carolina, Chapel Hill, NC†
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