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Maurex L, Zaboli G, Öhman A, Åsberg M, Leopardi R. The serotonin transporter gene polymorphism (5-HTTLPR) and affective symptoms among women diagnosed with borderline personality disorder. Eur Psychiatry 2020; 25:19-25. [DOI: 10.1016/j.eurpsy.2009.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 04/27/2009] [Accepted: 05/02/2009] [Indexed: 10/20/2022] Open
Abstract
AbstractGene variants of the serotonin transporter have been associated with vulnerability to affective disorders. In particular, the presence of one or two copies of the short (s) allele of the 5-HTTLPR polymorphism has been associated with reduced serotonin transporter expression and function, and vulnerability to affective disorders. To test for an association between variants of the serotonin transporter gene polymorphism (5-HTTLPR) and relevant clinical features of borderline personality disorder (BPD), a psychiatric disorder with symptoms characteristic for serotonin dysfunction, 77 women with BPD were genotyped in the 5-HTTLPR polymorphism. They rated their subjective experience of borderline-specific, depressive, anxious and obsessive-compulsive symptoms, and were interviewed about lifetime incidence of suicide attempts and self-harming acts. Carriers of two s alleles of the 5-HTTLPR reported more symptoms of borderline, depression, anxiety and obsessive-compulsive behaviours, but not of suicidal and self-injury behaviour, compared to carriers of a long (l) allele. This indicates that the 5-HTTLPR ss homozygous genotype might influence serotonin function affecting susceptibility to both borderline-specific, depressive, anxious and obsessive-compulsive symptoms in BPD, and leading to a more severe symptomatology related to these clinical features. Further, this suggests that 5-HTT gene variants may not be as influential on suicidal and self-injury behaviour in BPD.
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Parsa A, Fuchsberger C, Köttgen A, O’Seaghdha CM, Pattaro C, de Andrade M, Chasman DI, Teumer A, Endlich K, Olden M, Chen MH, Tin A, Kim YJ, Taliun D, Li M, Feitosa M, Gorski M, Yang Q, Hundertmark C, Foster MC, Glazer N, Isaacs A, Rao M, Smith AV, O’Connell JR, Struchalin M, Tanaka T, Li G, Hwang SJ, Atkinson EJ, Lohman K, Cornelis MC, Johansson Å, Tönjes A, Dehghan A, Couraki V, Holliday EG, Sorice R, Kutalik Z, Lehtimäki T, Esko T, Deshmukh H, Ulivi S, Chu AY, Murgia F, Trompet S, Imboden M, Kollerits B, Pistis G, Harris TB, Launer LJ, Aspelund T, Eiriksdottir G, Mitchell BD, Boerwinkle E, Schmidt H, Hofer E, Hu F, Demirkan A, Oostra BA, Turner ST, Ding J, Andrews JS, Freedman BI, Giulianini F, Koenig W, Illig T, Döring A, Wichmann HE, Zgaga L, Zemunik T, Boban M, Minelli C, Wheeler HE, Igl W, Zaboli G, Wild SH, Wright AF, Campbell H, Ellinghaus D, Nöthlings U, Jacobs G, Biffar R, Ernst F, Homuth G, Kroemer HK, Nauck M, Stracke S, Völker U, Völzke H, Kovacs P, Stumvoll M, Mägi R, Hofman A, Uitterlinden AG, Rivadeneira F, Aulchenko YS, Polasek O, Hastie N, Vitart V, Helmer C, Wang JJ, Stengel B, Ruggiero D, Bergmann S, Kähönen M, Viikari J, Nikopensius T, Province M, Colhoun H, Doney A, Robino A, Krämer BK, Portas L, Ford I, Buckley BM, Adam M, Thun GA, Paulweber B, Haun M, Sala C, Mitchell P, Ciullo M, Vollenweider P, Raitakari O, Metspalu A, Palmer C, Gasparini P, Pirastu M, Jukema JW, Probst-Hensch NM, Kronenberg F, Toniolo D, Gudnason V, Shuldiner AR, Coresh J, Schmidt R, Ferrucci L, van Duijn CM, Borecki I, Kardia SL, Liu Y, Curhan GC, Rudan I, Gyllensten U, Wilson JF, Franke A, Pramstaller PP, Rettig R, Prokopenko I, Witteman J, Hayward C, Ridker PM, Bochud M, Heid IM, Siscovick DS, Fox CS, Kao WL, Böger CA. Common variants in Mendelian kidney disease genes and their association with renal function. J Am Soc Nephrol 2013; 24:2105-17. [PMID: 24029420 PMCID: PMC3839542 DOI: 10.1681/asn.2012100983] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 07/10/2013] [Indexed: 12/28/2022] Open
Abstract
Many common genetic variants identified by genome-wide association studies for complex traits map to genes previously linked to rare inherited Mendelian disorders. A systematic analysis of common single-nucleotide polymorphisms (SNPs) in genes responsible for Mendelian diseases with kidney phenotypes has not been performed. We thus developed a comprehensive database of genes for Mendelian kidney conditions and evaluated the association between common genetic variants within these genes and kidney function in the general population. Using the Online Mendelian Inheritance in Man database, we identified 731 unique disease entries related to specific renal search terms and confirmed a kidney phenotype in 218 of these entries, corresponding to mutations in 258 genes. We interrogated common SNPs (minor allele frequency >5%) within these genes for association with the estimated GFR in 74,354 European-ancestry participants from the CKDGen Consortium. However, the top four candidate SNPs (rs6433115 at LRP2, rs1050700 at TSC1, rs249942 at PALB2, and rs9827843 at ROBO2) did not achieve significance in a stage 2 meta-analysis performed in 56,246 additional independent individuals, indicating that these common SNPs are not associated with estimated GFR. The effect of less common or rare variants in these genes on kidney function in the general population and disease-specific cohorts requires further research.
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Affiliation(s)
- Afshin Parsa
- Division of Nephrology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Christian Fuchsberger
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | - Anna Köttgen
- Renal Division, Freiburg University Clinic, Freiburg, Germany
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Conall M. O’Seaghdha
- National Heart, Lung, and Blood Institute's Framingham Heart Study and the Center for Population Studies, Framingham, Massachusetts
- Division of Nephrology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Cristian Pattaro
- Centre for Biomedicine, European Academy of Bozen/Bolzano, Bolzano, Italy
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Daniel I. Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Alexander Teumer
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Karlhans Endlich
- Institute of Anatomy and Cell Biology, University of Greifswald, Greifswald, Germany
| | - Matthias Olden
- Division of Nephrology, Department of Internal Medicine II, University Hospital Regensburg, Regensburg, Germany
- Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Ming-Huei Chen
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Adrienne Tin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Young J. Kim
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
- Genomics Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Daniel Taliun
- Centre for Biomedicine, European Academy of Bozen/Bolzano, Bolzano, Italy
| | - Man Li
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Mary Feitosa
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri
| | - Mathias Gorski
- Division of Nephrology, Department of Internal Medicine II, University Hospital Regensburg, Regensburg, Germany
- Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | | | - Meredith C. Foster
- National Heart, Lung, and Blood Institute's Framingham Heart Study and the Center for Population Studies, Framingham, Massachusetts
| | - Nicole Glazer
- Section of Preventive Medicine and Epidemiology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Aaron Isaacs
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Centre for Medical Systems Biology, Rotterdam, The Netherlands
| | - Madhumathi Rao
- Division of Nephrology, Tufts Evidence Practice Center, Tufts University School of Medicine, Tufts Medical Center, Boston, Massachusetts
| | - Albert V. Smith
- Research Institute, Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Jeffrey R. O’Connell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | - Maksim Struchalin
- Departments of Epidemiology and Biostatistics and Forensic Molecular Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Toshiko Tanaka
- Clinical Research Branch, National Institute of Aging, Baltimore Maryland
| | - Guo Li
- University of Washington, Seattle, Washington
| | - Shih-Jen Hwang
- National Heart, Lung, and Blood Institute's Framingham Heart Study and the Center for Population Studies, Framingham, Massachusetts
| | - Elizabeth J. Atkinson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Kurt Lohman
- Department of Epidemiology and Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Marilyn C. Cornelis
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts
| | - Åsa Johansson
- Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany
- Adiposity Diseases Integrated Research and Treatment Center, University of Leipzig, Leipzig, Germany
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Elizabeth G. Holliday
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, Australia
- Centre for Information-Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
| | - Rossella Sorice
- Adriano-Buzzati Traverso-CNR Institute of Genetics and Biophysics, Naples, Italy
| | - Zoltan Kutalik
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Terho Lehtimäki
- Fimlab Laboratories, Department of Clinical Chemistry, School of Medicine, University of Tampere, Tampere, Finland
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, Estonian Biocentre, University of Tartu, Tartu, Estonia
| | - Harshal Deshmukh
- Wellcome Trust Centre for Molecular Medicine, Clinical Research Centre, University of Dundee, Ninewells Hospital, Dundee, United Kingdom
| | - Sheila Ulivi
- IRCCS Burlo Garofolo Institute for Maternal and Child Health, University of Trieste, Trieste, Italy
| | - Audrey Y. Chu
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Stella Trompet
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Barbara Kollerits
- Division of Genetic Epidemiology, Innsbruck Medical University, Innsbruck, Austria
| | - Giorgio Pistis
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Tamara B. Harris
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, Bethesda, Maryland
| | - Lenore J. Launer
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, Bethesda, Maryland
| | - Thor Aspelund
- Research Institute, Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | | | - Braxton D. Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas
| | - Helena Schmidt
- Austrian Stroke Prevention Study, Department of Neurology, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Edith Hofer
- Austrian Stroke Prevention Study, Clinical Division of Neurogeriatrics, Department of Neurology, University Clinic of Neurology, Medical University of Graz, Graz, Austria
| | - Frank Hu
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts
| | - Ayse Demirkan
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Ben A. Oostra
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Stephen T. Turner
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Jingzhong Ding
- Division of Geriatrics, Department of Internal Medicine, Wake Forest School of Medicine, Wake Forest University, Winston-Salem, North Carolina
| | - Jeanette S. Andrews
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Wake Forest University, Winston-Salem, North Carolina
| | - Barry I. Freedman
- Division of Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Wake Forest University, Winston-Salem, North Carolina
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Wolfgang Koenig
- Department of Internal Medicine II, Ulm University Clinic, University of Ulm, Ulm, Germany
| | - Thomas Illig
- Hanover Unified Biobank, Hanover Medical School, Hanover, Germany
- Research Unit of Molecular Epidemiology, German Research Center for Environmental Health, Neuherberg, Germany
| | - Angela Döring
- Institute of Epidemiology I and II, German Research Center for Environmental Health, Neuherberg, Germany
| | - H.-Erich Wichmann
- Institute of Epidemiology I and II, German Research Center for Environmental Health, Neuherberg, Germany
- Institute for Medical Informatics, Biometry, and Epidemiology, Ludwig-Maximilians-University, Munich, Germany
- Grosshadern Clinic, Neuherberg, Germany
| | - Lina Zgaga
- Center for Population Health Sciences, University of Edinburgh Medical School, Edinburgh, Scotland, United Kingdom
| | - Tatijana Zemunik
- Croatian Centre for Global Health, University of Split Medical School, Split, Croatia
| | - Mladen Boban
- Croatian Centre for Global Health, University of Split Medical School, Split, Croatia
| | - Cosetta Minelli
- Centre for Biomedicine, European Academy of Bozen/Bolzano, Bolzano, Italy
| | - Heather E. Wheeler
- Department of Genetics, Stanford University, Stanford, California
- Department of Medicine, University of Chicago, Chicago, Illinois
| | - Wilmar Igl
- Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ghazal Zaboli
- Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sarah H. Wild
- Center for Population Health Sciences, University of Edinburgh Medical School, Edinburgh, Scotland, United Kingdom
| | - Alan F. Wright
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, United Kingdom
| | - Harry Campbell
- Center for Population Health Sciences, University of Edinburgh Medical School, Edinburgh, Scotland, United Kingdom
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Ute Nöthlings
- PopGen Biobank, Schleswig-Holstein University Hospital, Kiel, Germany
- Institute for Epidemiology, University of Kiel, Kiel, Germany
- Department of Nutrition and Food Sciences, University of Bonn, Bonn, Germany
| | - Gunnar Jacobs
- PopGen Biobank, Schleswig-Holstein University Hospital, Kiel, Germany
- Institute for Epidemiology, University of Kiel, Kiel, Germany
| | - Reiner Biffar
- Clinic for Prosthodontic Dentistry, Gerostomatology, and Material Science, University of Greifswald, Greifswald, Germany
| | - Florian Ernst
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Heyo K. Kroemer
- Institute of Pharmacology, University of Greifswald, Greifswald, Germany
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University of Greifswald, Greifswald, Germany
| | - Sylvia Stracke
- Clinic for Internal Medicine A, University of Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University of Greifswald, Greifswald, Germany
| | - Peter Kovacs
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig, Leipzig, Germany
- Adiposity Diseases Integrated Research and Treatment Center, University of Leipzig, Leipzig, Germany
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Yurii S. Aulchenko
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ozren Polasek
- Croatian Centre for Global Health, University of Split Medical School, Split, Croatia
| | - Nick Hastie
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, United Kingdom
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, United Kingdom
| | - Catherine Helmer
- INSERM U897, Institute of Public Health, Victor Segalen Bordeaux II University, Bordeaux, France
- Victor Segalen Bordeaux II University, Bordeaux, France
| | - Jie Jin Wang
- Centre for Vision Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Sydney, Australia
- Centre for Eye Research Australia, University of Melbourne, East Melbourne, Australia
| | - Bénédicte Stengel
- INSERM UMRS 1018, Villejuif, France
- UMRS 1018, University of Paris-Sud, Paris, France
| | - Daniela Ruggiero
- Adriano-Buzzati Traverso-CNR Institute of Genetics and Biophysics, Naples, Italy
| | - Sven Bergmann
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, School of Medicine, University of Tampere, Tampere, Finland
| | - Jorma Viikari
- Department of Medicine, Turku University Hospital, University of Turku, Turku, Finland
| | - Tiit Nikopensius
- Institute of Molecular and Cell Biology, Estonian Biocentre, University of Tartu, Tartu, Estonia
| | - Michael Province
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri
| | - Helen Colhoun
- Wellcome Trust Centre for Molecular Medicine, Clinical Research Centre, University of Dundee, Ninewells Hospital, Dundee, United Kingdom
| | - Alex Doney
- National Health Service Tayside, Wellcome Trust Centre for Molecular Medicine, Clinical Research Centre, Ninewells Hospital, Dundee, United Kingdom
| | - Antonietta Robino
- IRCCS Burlo Garofolo Institute for Maternal and Child Health, University of Trieste, Trieste, Italy
| | - Bernhard K. Krämer
- Fifth Department of Medicine, Mannheim University Medical Centre, Mannheim, Germany
| | - Laura Portas
- CNR Institute of Population Genetics, Sassari, Italy
| | - Ian Ford
- Robertson Centre for Biostatistics, University of Glasgow, Glasgow, United Kingdom
| | - Brendan M. Buckley
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland
| | - Martin Adam
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Gian-Andri Thun
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Bernhard Paulweber
- First Department of Internal Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Margot Haun
- Division of Genetic Epidemiology, Innsbruck Medical University, Innsbruck, Austria
| | - Cinzia Sala
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Paul Mitchell
- Centre for Vision Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Sydney, Australia
| | - Marina Ciullo
- Adriano-Buzzati Traverso-CNR Institute of Genetics and Biophysics, Naples, Italy
| | - Peter Vollenweider
- Department of Internal Medicine, Vaudois University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, Estonian Biocentre, University of Tartu, Tartu, Estonia
| | - Colin Palmer
- Biomedical Research Institute, University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Paolo Gasparini
- IRCCS Burlo Garofolo Institute for Maternal and Child Health, University of Trieste, Trieste, Italy
| | - Mario Pirastu
- CNR Institute of Population Genetics, Sassari, Italy
| | - J. Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Interuniversity Cardiology Institute of the Netherlands, Utrecht, The Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden, The Netherlands
- Durrer Center for Cardiogenetic Research, Amsterdam, The Netherlands
| | - Nicole M. Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Innsbruck Medical University, Innsbruck, Austria
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
- CNR Institute of Molecular Genetics, Pavia, Italy
| | - Vilmundur Gudnason
- Research Institute, Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Alan R. Shuldiner
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
- Geriatric Research and Education Clinical Center, Veterans Affairs Medical Center, Baltimore, Maryland
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Welch Center for Prevention, Epidemiology, and Clinical Research, Baltimore, Maryland
| | - Reinhold Schmidt
- Austrian Stroke Prevention Study, Clinical Division of Neurogeriatrics, Department of Neurology, University Clinic of Neurology, Medical University of Graz, Graz, Austria
| | - Luigi Ferrucci
- Clinical Research Branch, National Institute of Aging, Baltimore Maryland
| | - Cornelia M. van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Centre for Medical Systems Biology, Rotterdam, The Netherlands
- Netherlands Consortium for Healthy Aging, Netherlands Genomics Initiative, Leiden, the Netherlands
| | - Ingrid Borecki
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri
| | - Sharon L.R. Kardia
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Gary C. Curhan
- Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Igor Rudan
- Center for Population Health Sciences, University of Edinburgh Medical School, Edinburgh, Scotland, United Kingdom
| | - Ulf Gyllensten
- Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - James F. Wilson
- Center for Population Health Sciences, University of Edinburgh Medical School, Edinburgh, Scotland, United Kingdom
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | | | - Rainer Rettig
- Institute of Physiology, University of Greifswald, Karlsburg, Germany
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford, United Kingdom
| | - Jacqueline Witteman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, United Kingdom
| | - Paul M. Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Murielle Bochud
- University Institute of Social and Preventive Medicine, Vaudois University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Iris M. Heid
- Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany; and
| | | | - Caroline S. Fox
- National Heart, Lung, and Blood Institute's Framingham Heart Study and the Center for Population Studies, Framingham, Massachusetts
- Division of Endocrinology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - W. Linda Kao
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Welch Center for Prevention, Epidemiology, and Clinical Research, Baltimore, Maryland
| | - Carsten A. Böger
- Division of Nephrology, Department of Internal Medicine II, University Hospital Regensburg, Regensburg, Germany
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Chasman DI, Fuchsberger C, Pattaro C, Teumer A, Böger CA, Endlich K, Olden M, Chen MH, Tin A, Taliun D, Li M, Gao X, Gorski M, Yang Q, Hundertmark C, Foster MC, O'Seaghdha CM, Glazer N, Isaacs A, Liu CT, Smith AV, O'Connell JR, Struchalin M, Tanaka T, Li G, Johnson AD, Gierman HJ, Feitosa MF, Hwang SJ, Atkinson EJ, Lohman K, Cornelis MC, Johansson A, Tönjes A, Dehghan A, Lambert JC, Holliday EG, Sorice R, Kutalik Z, Lehtimäki T, Esko T, Deshmukh H, Ulivi S, Chu AY, Murgia F, Trompet S, Imboden M, Coassin S, Pistis G, Harris TB, Launer LJ, Aspelund T, Eiriksdottir G, Mitchell BD, Boerwinkle E, Schmidt H, Cavalieri M, Rao M, Hu F, Demirkan A, Oostra BA, de Andrade M, Turner ST, Ding J, Andrews JS, Freedman BI, Giulianini F, Koenig W, Illig T, Meisinger C, Gieger C, Zgaga L, Zemunik T, Boban M, Minelli C, Wheeler HE, Igl W, Zaboli G, Wild SH, Wright AF, Campbell H, Ellinghaus D, Nöthlings U, Jacobs G, Biffar R, Ernst F, Homuth G, Kroemer HK, Nauck M, Stracke S, Völker U, Völzke H, Kovacs P, Stumvoll M, Mägi R, Hofman A, Uitterlinden AG, Rivadeneira F, Aulchenko YS, Polasek O, Hastie N, Vitart V, Helmer C, Wang JJ, Stengel B, Ruggiero D, Bergmann S, Kähönen M, Viikari J, Nikopensius T, Province M, Ketkar S, Colhoun H, Doney A, Robino A, Krämer BK, Portas L, Ford I, Buckley BM, Adam M, Thun GA, Paulweber B, Haun M, Sala C, Mitchell P, Ciullo M, Kim SK, Vollenweider P, Raitakari O, Metspalu A, Palmer C, Gasparini P, Pirastu M, Jukema JW, Probst-Hensch NM, Kronenberg F, Toniolo D, Gudnason V, Shuldiner AR, Coresh J, Schmidt R, Ferrucci L, Siscovick DS, van Duijn CM, Borecki IB, Kardia SLR, Liu Y, Curhan GC, Rudan I, Gyllensten U, Wilson JF, Franke A, Pramstaller PP, Rettig R, Prokopenko I, Witteman J, Hayward C, Ridker PM, Parsa A, Bochud M, Heid IM, Kao WHL, Fox CS, Köttgen A. Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function. Hum Mol Genet 2012; 21:5329-43. [PMID: 22962313 DOI: 10.1093/hmg/dds369] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P = 5.6 × 10(-9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 × 10(-4)-2.2 × 10(-7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.
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Affiliation(s)
- Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
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Ameur A, Enroth S, Johansson Å, Zaboli G, Igl W, Johansson A, Rivas M, Daly M, Schmitz G, Hicks A, Meitinger T, Feuk L, van Duijn C, Oostra B, Pramstaller P, Rudan I, Wright A, Wilson J, Campbell H, Gyllensten U. Genetic adaptation of fatty-acid metabolism: a human-specific haplotype increasing the biosynthesis of long-chain omega-3 and omega-6 fatty acids. Am J Hum Genet 2012; 90:809-20. [PMID: 22503634 DOI: 10.1016/j.ajhg.2012.03.014] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 02/03/2012] [Accepted: 03/15/2012] [Indexed: 10/28/2022] Open
Abstract
Omega-3 and omega-6 long-chain polyunsaturated fatty acids (LC-PUFAs) are essential for the development and function of the human brain. They can be obtained directly from food, e.g., fish, or synthesized from precursor molecules found in vegetable oils. To determine the importance of genetic variability to fatty-acid biosynthesis, we studied FADS1 and FADS2, which encode rate-limiting enzymes for fatty-acid conversion. We performed genome-wide genotyping (n = 5,652 individuals) and targeted resequencing (n = 960 individuals) of the FADS region in five European population cohorts. We also analyzed available genomic data from human populations, archaic hominins, and more distant primates. Our results show that present-day humans have two common FADS haplotypes-defined by 28 closely linked SNPs across 38.9 kb-that differ dramatically in their ability to generate LC-PUFAs. No independent effects on FADS activity were seen for rare SNPs detected by targeted resequencing. The more efficient, evolutionarily derived haplotype appeared after the lineage split leading to modern humans and Neanderthals and shows evidence of positive selection. This human-specific haplotype increases the efficiency of synthesizing essential long-chain fatty acids from precursors and thereby might have provided an advantage in environments with limited access to dietary LC-PUFAs. In the modern world, this haplotype has been associated with lifestyle-related diseases, such as coronary artery disease.
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5
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Pattaro C, Köttgen A, Teumer A, Garnaas M, Böger CA, Fuchsberger C, Olden M, Chen MH, Tin A, Taliun D, Li M, Gao X, Gorski M, Yang Q, Hundertmark C, Foster MC, O'Seaghdha CM, Glazer N, Isaacs A, Liu CT, Smith AV, O'Connell JR, Struchalin M, Tanaka T, Li G, Johnson AD, Gierman HJ, Feitosa M, Hwang SJ, Atkinson EJ, Lohman K, Cornelis MC, Johansson Å, Tönjes A, Dehghan A, Chouraki V, Holliday EG, Sorice R, Kutalik Z, Lehtimäki T, Esko T, Deshmukh H, Ulivi S, Chu AY, Murgia F, Trompet S, Imboden M, Kollerits B, Pistis G, Harris TB, Launer LJ, Aspelund T, Eiriksdottir G, Mitchell BD, Boerwinkle E, Schmidt H, Cavalieri M, Rao M, Hu FB, Demirkan A, Oostra BA, de Andrade M, Turner ST, Ding J, Andrews JS, Freedman BI, Koenig W, Illig T, Döring A, Wichmann HE, Kolcic I, Zemunik T, Boban M, Minelli C, Wheeler HE, Igl W, Zaboli G, Wild SH, Wright AF, Campbell H, Ellinghaus D, Nöthlings U, Jacobs G, Biffar R, Endlich K, Ernst F, Homuth G, Kroemer HK, Nauck M, Stracke S, Völker U, Völzke H, Kovacs P, Stumvoll M, Mägi R, Hofman A, Uitterlinden AG, Rivadeneira F, Aulchenko YS, Polasek O, Hastie N, Vitart V, Helmer C, Wang JJ, Ruggiero D, Bergmann S, Kähönen M, Viikari J, Nikopensius T, Province M, Ketkar S, Colhoun H, Doney A, Robino A, Giulianini F, Krämer BK, Portas L, Ford I, Buckley BM, Adam M, Thun GA, Paulweber B, Haun M, Sala C, Metzger M, Mitchell P, Ciullo M, Kim SK, Vollenweider P, Raitakari O, Metspalu A, Palmer C, Gasparini P, Pirastu M, Jukema JW, Probst-Hensch NM, Kronenberg F, Toniolo D, Gudnason V, Shuldiner AR, Coresh J, Schmidt R, Ferrucci L, Siscovick DS, van Duijn CM, Borecki I, Kardia SLR, Liu Y, Curhan GC, Rudan I, Gyllensten U, Wilson JF, Franke A, Pramstaller PP, Rettig R, Prokopenko I, Witteman JCM, Hayward C, Ridker P, Parsa A, Bochud M, Heid IM, Goessling W, Chasman DI, Kao WHL, Fox CS. Genome-wide association and functional follow-up reveals new loci for kidney function. PLoS Genet 2012; 8:e1002584. [PMID: 22479191 PMCID: PMC3315455 DOI: 10.1371/journal.pgen.1002584] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [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: 10/01/2011] [Accepted: 01/22/2012] [Indexed: 01/06/2023] Open
Abstract
Chronic kidney disease (CKD) is an important public health problem with a genetic component. We performed genome-wide association studies in up to 130,600 European ancestry participants overall, and stratified for key CKD risk factors. We uncovered 6 new loci in association with estimated glomerular filtration rate (eGFR), the primary clinical measure of CKD, in or near MPPED2, DDX1, SLC47A1, CDK12, CASP9, and INO80. Morpholino knockdown of mpped2 and casp9 in zebrafish embryos revealed podocyte and tubular abnormalities with altered dextran clearance, suggesting a role for these genes in renal function. By providing new insights into genes that regulate renal function, these results could further our understanding of the pathogenesis of CKD.
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Affiliation(s)
- Cristian Pattaro
- Institute of Genetic Medicine, European Academy of Bozen/Bolzano (EURAC) and Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Anna Köttgen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Renal Division, Freiburg University Clinic, Freiburg, Germany
| | - Alexander Teumer
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Maija Garnaas
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Carsten A. Böger
- Department of Internal Medicine II, University Medical Center Regensburg, Regensburg, Germany
| | - Christian Fuchsberger
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Matthias Olden
- Department of Internal Medicine II, University Hospital Regensburg, Regensburg, Germany
- Department of Epidemiology and Preventive Medicine, Regensburg University Medical Center, Regensburg, Germany
| | - Ming-Huei Chen
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Adrienne Tin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Daniel Taliun
- Institute of Genetic Medicine, European Academy of Bozen/Bolzano (EURAC) and Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Man Li
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Xiaoyi Gao
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Mathias Gorski
- Department of Epidemiology and Preventive Medicine, University Hospital Regensburg, Regensburg, Germany
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | | | - Meredith C. Foster
- National Heart, Lung, and Blood Institute's Framingham Heart Study and the Center for Population Studies, Framingham, Massachusetts, United States of America
| | - Conall M. O'Seaghdha
- National Heart, Lung, and Blood Institute's Framingham Heart Study and the Center for Population Studies, Framingham, Massachusetts, United States of America
- Division of Nephrology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nicole Glazer
- Section of Preventive Medicine and Epidemiology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Aaron Isaacs
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Centre for Medical Systems Biology, Leiden, The Netherlands
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Albert V. Smith
- Icelandic Heart Association, Research Institute, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Jeffrey R. O'Connell
- Department of Medicine, University of Maryland Medical School, Baltimore, Maryland, United States of America
| | - Maksim Struchalin
- Department of Epidemiology and Biostatistics and Department of Forensic Molecular Biology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Toshiko Tanaka
- Clinical Research Branch, National Institute of Aging, Baltimore, Maryland, United States of America
| | - Guo Li
- University of Washington, Seattle, Washington, United States of America
| | - Andrew D. Johnson
- National Heart, Lung, and Blood Institute's Framingham Heart Study and the Center for Population Studies, Framingham, Massachusetts, United States of America
| | - Hinco J. Gierman
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Mary Feitosa
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Shih-Jen Hwang
- National Heart, Lung, and Blood Institute's Framingham Heart Study and the Center for Population Studies, Framingham, Massachusetts, United States of America
| | - Elizabeth J. Atkinson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Kurt Lohman
- Department of Epidemiology and Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Marilyn C. Cornelis
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Åsa Johansson
- Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Anke Tönjes
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Elizabeth G. Holliday
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine and Public Health, University of Newcastle, Newcastle, Australia
- Centre for Information-based Medicine, Hunter Medical Research Institute, Newcastle, Australia
| | - Rossella Sorice
- Institute of Genetics and Biophysics “Adriano-Buzzati Traverso”–CNR, Napoli, Italy
| | - Zoltan Kutalik
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, University of Tampere and Tampere University Hospital, Centre for Laboratory Medicine Tampere Finn-Medi 2, Tampere, Finland
| | - Tõnu Esko
- Estonian Genome Center of University of Tartu (EGCUT), Tartu, Estonia
- Estonian Biocenter and Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Harshal Deshmukh
- Wellcome Trust Centre for Molecular Medicine, Clinical Research Centre, Ninewells Hospital, University of Dundee, Dundee, United Kingdom
| | - Sheila Ulivi
- Institute for Maternal and Child Health – IRCCS “Burlo Garofolo”, Trieste, Italy
| | - Audrey Y. Chu
- Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | | | - Stella Trompet
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Medea Imboden
- Unit of Chronic Disease Epidemiology, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Barbara Kollerits
- Division of Genetic Epidemiology, Innsbruck Medical University, Innsbruck, Austria
| | - Giorgio Pistis
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy
| | | | | | | | | | - Tamara B. Harris
- Laboratory of Epidemiology, Demography, and Biometry, NIA, Bethesda, Maryland, United States of America
| | - Lenore J. Launer
- Laboratory of Epidemiology, Demography, and Biometry, NIA, Bethesda, Maryland, United States of America
| | - Thor Aspelund
- Icelandic Heart Association, Research Institute, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | | | - Braxton D. Mitchell
- Department of Medicine, University of Maryland Medical School, Baltimore, Maryland, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Helena Schmidt
- Austrian Stroke Prevention Study, Institute of Molecular Biology and Biochemistry and Department of Neurology, Medical University Graz, Graz, Austria
| | - Margherita Cavalieri
- Austrian Stroke Prevention Study, University Clinic of Neurology, Department of Special Neurology, Medical University Graz, Graz, Austria
| | - Madhumathi Rao
- Division of Nephrology/Tufts Evidence Practice Center, Tufts University School of Medicine, Tufts Medical Center, Boston, Massachusetts, United States of America
| | - Frank B. Hu
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Ayse Demirkan
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ben A. Oostra
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Stephen T. Turner
- Department of Internal Medicine, Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Jingzhong Ding
- Department of Internal Medicine/Geriatrics, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Jeanette S. Andrews
- Department of Biostatistical Sciences, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Barry I. Freedman
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | | | - Thomas Illig
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Angela Döring
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - H.-Erich Wichmann
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry, and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- Klinikum Grosshadern, Neuherberg, Germany
| | - Ivana Kolcic
- Croatian Centre for Global Health, University of Split Medical School, Split, Croatia
| | - Tatijana Zemunik
- Croatian Centre for Global Health, University of Split Medical School, Split, Croatia
| | - Mladen Boban
- Croatian Centre for Global Health, University of Split Medical School, Split, Croatia
| | - Cosetta Minelli
- Institute of Genetic Medicine, European Academy of Bozen/Bolzano (EURAC) and Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Heather E. Wheeler
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Wilmar Igl
- Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Ghazal Zaboli
- Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Sarah H. Wild
- Center for Population Health Sciences, University of Edinburgh Medical School, Edinburgh, United Kingdom
| | - Alan F. Wright
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, United Kingdom
| | - Harry Campbell
- Center for Population Health Sciences, University of Edinburgh Medical School, Edinburgh, United Kingdom
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Ute Nöthlings
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
- popgen Biobank, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Gunnar Jacobs
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
- popgen Biobank, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Reiner Biffar
- Clinic for Prosthodontic Dentistry, Gerostomatology, and Material Science, University of Greifswald, Greifswald, Germany
| | - Karlhans Endlich
- Institute of Anatomy and Cell Biology, University of Greifswald, Greifswald, Germany
| | - Florian Ernst
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Heyo K. Kroemer
- Institute of Pharmacology, University of Greifswald, Greifswald, Germany
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Sylvia Stracke
- Clinic for Internal Medicine A, University of Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University of Greifswald, Greifswald, Germany
| | - Peter Kovacs
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Michael Stumvoll
- Department of Medicine, University of Leipzig, Leipzig, Germany
- IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Reedik Mägi
- Estonian Genome Center of University of Tartu (EGCUT), Tartu, Estonia
- Wellcome Trust Centre for Human Genetics and Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford, United Kingdom
| | - Albert Hofman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Andre G. Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yurii S. Aulchenko
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ozren Polasek
- Croatian Centre for Global Health, Faculty of Medicine, University of Split, Split, Croatia
| | - Nick Hastie
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, United Kingdom
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, United Kingdom
| | - Catherine Helmer
- INSERM U897, Université Victor Ségalen Bordeaux 2, ISPED, Bordeaux, France
- Université Bordeaux 2 Victor Segalen, Bordeaux, France
| | - Jie Jin Wang
- Centre for Vision Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Sydney, Australia
- Centre for Eye Research Australia (CERA), University of Melbourne, Melbourne, Australia
| | - Daniela Ruggiero
- Institute of Genetics and Biophysics “Adriano-Buzzati Traverso”–CNR, Napoli, Italy
| | - Sven Bergmann
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mika Kähönen
- Department of Clinical Physiology, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Jorma Viikari
- Department of Medicine, University of Turku and Turku University Hospital, Turku, Finland
| | - Tiit Nikopensius
- Estonian Biocenter and Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Michael Province
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Shamika Ketkar
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Helen Colhoun
- Wellcome Trust Centre for Molecular Medicine, Clinical Research Centre, Ninewells Hospital, University of Dundee, Dundee, United Kingdom
| | - Alex Doney
- NHS Tayside, Wellcome Trust Centre for Molecular Medicine, Clinical Research Centre, Ninewells Hospital, University of Dundee, Dundee, United Kingdom
| | - Antonietta Robino
- Institute for Maternal and Child Health, IRCCS “Burlo Garofolo,” University of Trieste, Trieste, Italy
| | - Franco Giulianini
- Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Bernhard K. Krämer
- University Medical Centre Mannheim, 5th Department of Medicine, Mannheim, Germany
| | - Laura Portas
- Institute of Population Genetics – CNR, Sassari, Italy
| | - Ian Ford
- Robertson Centre for Biostatistics, University of Glasgow, Glasgow, United Kingdom
| | - Brendan M. Buckley
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland
| | - Martin Adam
- Unit of Chronic Disease Epidemiology, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Gian-Andri Thun
- Unit of Chronic Disease Epidemiology, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Bernhard Paulweber
- First Department of Internal Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Margot Haun
- Division of Genetic Epidemiology, Innsbruck Medical University, Innsbruck, Austria
| | - Cinzia Sala
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy
| | - Marie Metzger
- Inserm UMRS 1018, CESP Team 10, Université Paris Sud, Villejuif, France
| | - Paul Mitchell
- Centre for Vision Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Sydney, Australia
| | - Marina Ciullo
- Institute of Genetics and Biophysics “Adriano-Buzzati Traverso”–CNR, Napoli, Italy
| | - Stuart K. Kim
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Peter Vollenweider
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, Department of Clinical Physiology, Turku University Hospital, University of Turku, Turku, Finland
| | - Andres Metspalu
- Estonian Genome Center of University of Tartu (EGCUT), Tartu, Estonia
- Estonian Biocenter and Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Colin Palmer
- Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
| | - Paolo Gasparini
- Institute for Maternal and Child Health, IRCCS “Burlo Garofolo,” University of Trieste, Trieste, Italy
| | - Mario Pirastu
- Institute of Population Genetics – CNR, Sassari, Italy
| | - J. Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
- Interuniversity Cardiology Institute of the Netherlands (ICIN), Utrecht, The Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden, The Netherlands
- Durrer Center for Cardiogenetic Research, Amsterdam, The Netherlands
| | - Nicole M. Probst-Hensch
- Unit of Chronic Disease Epidemiology, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Innsbruck Medical University, Innsbruck, Austria
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy
| | - Vilmundur Gudnason
- Icelandic Heart Association, Research Institute, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Alan R. Shuldiner
- Department of Medicine, University of Maryland Medical School, Baltimore, Maryland, United States of America
- Geriatric Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, Maryland, United States of America
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Welch Center for Prevention, Epidemiology, and Clinical Research, Baltimore, Maryland, United States of America
| | - Reinhold Schmidt
- Austrian Stroke Prevention Study, University Clinic of Neurology, Department of Special Neurology, Medical University Graz, Graz, Austria
| | - Luigi Ferrucci
- Clinical Research Branch, National Institute of Aging, Baltimore, Maryland, United States of America
| | | | - Cornelia M. van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ingrid Borecki
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Gary C. Curhan
- Brigham and Women's Hospital and Channing Laboratory, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Igor Rudan
- Center for Population Health Sciences, University of Edinburgh Medical School, Edinburgh, United Kingdom
| | - Ulf Gyllensten
- Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - James F. Wilson
- Center for Population Health Sciences, University of Edinburgh Medical School, Edinburgh, United Kingdom
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Peter P. Pramstaller
- Institute of Genetic Medicine, European Academy of Bozen/Bolzano (EURAC) and Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Rainer Rettig
- Institute of Physiology, University of Greifswald, Greifswald, Germany
| | - Inga Prokopenko
- Wellcome Trust Centre for Human Genetics and Oxford Centre for Diabetes, Endocrinology, and Metabolism, University of Oxford, Oxford, United Kingdom
| | | | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, United Kingdom
| | - Paul Ridker
- Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Afshin Parsa
- Division of Nephrology, University of Maryland Medical School, Baltimore, Maryland, United States of America
| | - Murielle Bochud
- University Institute of Social and Preventive Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Epalinges, Switzerland
| | - Iris M. Heid
- Department of Epidemiology and Preventive Medicine, University Hospital Regensburg, Regensburg, Germany
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Wolfram Goessling
- Divisions of Genetics and Gastroenterology, Department of Internal Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, United States of America
| | - Daniel I. Chasman
- Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - W. H. Linda Kao
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- Welch Center for Prevention, Epidemiology, and Clinical Research, Baltimore, Maryland, United States of America
| | - Caroline S. Fox
- National Heart, Lung, and Blood Institute's Framingham Heart Study and the Center for Population Studies, Framingham, Massachusetts, United States of America
- Division of Endocrinology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
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6
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Demirkan A, van Duijn CM, Ugocsai P, Isaacs A, Pramstaller PP, Liebisch G, Wilson JF, Johansson Å, Rudan I, Aulchenko YS, Kirichenko AV, Janssens ACJW, Jansen RC, Gnewuch C, Domingues FS, Pattaro C, Wild SH, Jonasson I, Polasek O, Zorkoltseva IV, Hofman A, Karssen LC, Struchalin M, Floyd J, Igl W, Biloglav Z, Broer L, Pfeufer A, Pichler I, Campbell S, Zaboli G, Kolcic I, Rivadeneira F, Huffman J, Hastie ND, Uitterlinden A, Franke L, Franklin CS, Vitart V, Nelson CP, Preuss M, Bis JC, O'Donnell CJ, Franceschini N, Witteman JCM, Axenovich T, Oostra BA, Meitinger T, Hicks AA, Hayward C, Wright AF, Gyllensten U, Campbell H, Schmitz G. Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations. PLoS Genet 2012; 8:e1002490. [PMID: 22359512 PMCID: PMC3280968 DOI: 10.1371/journal.pgen.1002490] [Citation(s) in RCA: 149] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 12/05/2011] [Indexed: 11/19/2022] Open
Abstract
Phospho- and sphingolipids are crucial cellular and intracellular compounds. These lipids are required for active transport, a number of enzymatic processes, membrane formation, and cell signalling. Disruption of their metabolism leads to several diseases, with diverse neurological, psychiatric, and metabolic consequences. A large number of phospholipid and sphingolipid species can be detected and measured in human plasma. We conducted a meta-analysis of five European family-based genome-wide association studies (N = 4034) on plasma levels of 24 sphingomyelins (SPM), 9 ceramides (CER), 57 phosphatidylcholines (PC), 20 lysophosphatidylcholines (LPC), 27 phosphatidylethanolamines (PE), and 16 PE-based plasmalogens (PLPE), as well as their proportions in each major class. This effort yielded 25 genome-wide significant loci for phospholipids (smallest P-value = 9.88×10−204) and 10 loci for sphingolipids (smallest P-value = 3.10×10−57). After a correction for multiple comparisons (P-value<2.2×10−9), we observed four novel loci significantly associated with phospholipids (PAQR9, AGPAT1, PKD2L1, PDXDC1) and two with sphingolipids (PLD2 and APOE) explaining up to 3.1% of the variance. Further analysis of the top findings with respect to within class molar proportions uncovered three additional loci for phospholipids (PNLIPRP2, PCDH20, and ABDH3) suggesting their involvement in either fatty acid elongation/saturation processes or fatty acid specific turnover mechanisms. Among those, 14 loci (KCNH7, AGPAT1, PNLIPRP2, SYT9, FADS1-2-3, DLG2, APOA1, ELOVL2, CDK17, LIPC, PDXDC1, PLD2, LASS4, and APOE) mapped into the glycerophospholipid and 12 loci (ILKAP, ITGA9, AGPAT1, FADS1-2-3, APOA1, PCDH20, LIPC, PDXDC1, SGPP1, APOE, LASS4, and PLD2) to the sphingolipid pathways. In large meta-analyses, associations between FADS1-2-3 and carotid intima media thickness, AGPAT1 and type 2 diabetes, and APOA1 and coronary artery disease were observed. In conclusion, our study identified nine novel phospho- and sphingolipid loci, substantially increasing our knowledge of the genetic basis for these traits. Phospho- and sphingolipids are integral to membrane formation and are involved in crucial cellular functions such as signalling, membrane fluidity, membrane protein trafficking, neurotransmission, and receptor trafficking. In addition to severe monogenic diseases resulting from defective phospho- and sphingolipid function and metabolism, the evidence suggests that variations in these lipid levels at the population level are involved in the determination of cardiovascular and neurologic traits and subsequent disease. We took advantage of modern laboratory methods, including microarray-based genotyping and electrospray ionization tandem mass spectrometry, to hunt for genetic variation influencing the levels of more than 350 phospho- and sphingolipid phenotypes. We identified nine novel loci, in addition to confirming a number of previously described loci. Several other genetic regions provided substantial evidence of their involvement in these traits. All of these loci are strong candidates for further research in the field of lipid biology and are likely to yield considerable insights into the complex metabolic pathways underlying circulating phospho- and sphingolipid levels. Understanding these mechanisms might help to illuminate factors leading to the development of common cardiovascular and neurological diseases and might provide molecular targets for the development of new therapies.
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Affiliation(s)
- Ayşe Demirkan
- Genetic Epidemiology Unit, Departments of Epidemiology and Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Cornelia M. van Duijn
- Genetic Epidemiology Unit, Departments of Epidemiology and Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
- Centre for Medical Sytems Biology, Leiden, The Netherlands
- Netherlands Consortium for Healthy Aging, Netherlands Genomics Initiative, Leiden, The Netherlands
| | - Peter Ugocsai
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Aaron Isaacs
- Genetic Epidemiology Unit, Departments of Epidemiology and Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
- Centre for Medical Sytems Biology, Leiden, The Netherlands
- * E-mail:
| | - Peter P. Pramstaller
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy
- Department of Neurology, General Central Hospital, Bolzano, Italy
- Department of Neurology, University of Lubeck, Lubeck, Germany
| | - Gerhard Liebisch
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - James F. Wilson
- Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh, United Kingdom
| | - Åsa Johansson
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Igor Rudan
- Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh, United Kingdom
- Institute for Clinical Medical Research, University Hospital “Sestre Milosrdnice”, Zagreb, Croatia
- Croatian Centre for Global Health, Faculty of Medicine, University of Split, Split, Croatia
| | - Yurii S. Aulchenko
- Genetic Epidemiology Unit, Departments of Epidemiology and Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anatoly V. Kirichenko
- Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - Ritsert C. Jansen
- Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Carsten Gnewuch
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | | | - Cristian Pattaro
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy
| | - Sarah H. Wild
- Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh, United Kingdom
| | - Inger Jonasson
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
- Croatian Centre for Global Health, Faculty of Medicine, University of Split, Split, Croatia
| | - Ozren Polasek
- Croatian Centre for Global Health, Faculty of Medicine, University of Split, Split, Croatia
| | - Irina V. Zorkoltseva
- Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Albert Hofman
- Netherlands Consortium for Healthy Aging, Netherlands Genomics Initiative, Leiden, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lennart C. Karssen
- Genetic Epidemiology Unit, Departments of Epidemiology and Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Maksim Struchalin
- Genetic Epidemiology Unit, Departments of Epidemiology and Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - James Floyd
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Wilmar Igl
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Zrinka Biloglav
- Andrija Stampar School of Public Health, Faculty of Medicine, University of Zagreb, Zagreb, Croatia
| | - Linda Broer
- Genetic Epidemiology Unit, Departments of Epidemiology and Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Arne Pfeufer
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy
| | - Irene Pichler
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy
| | - Susan Campbell
- Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh, United Kingdom
| | - Ghazal Zaboli
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Ivana Kolcic
- Croatian Centre for Global Health, Faculty of Medicine, University of Split, Split, Croatia
| | - Fernando Rivadeneira
- Netherlands Consortium for Healthy Aging, Netherlands Genomics Initiative, Leiden, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jennifer Huffman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Nicholas D. Hastie
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Andre Uitterlinden
- Netherlands Consortium for Healthy Aging, Netherlands Genomics Initiative, Leiden, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lude Franke
- Genetics Department, University Medical Centre Groningen and University of Groningen, Groningen, The Netherlands
| | | | - Veronique Vitart
- Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh, United Kingdom
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | | | - Christopher P. Nelson
- Department of Cardiovascular Science, University of Leicester, Leicester, United Kingdom
| | - Michael Preuss
- Institut fur Medizinische Biometrie und Statistik and Medizinische Klinik II, Universitat zu Lubeck, Lubeck, Germany
| | | | - Joshua C. Bis
- Cardiovascular Health Research Unit and Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Christopher J. O'Donnell
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | | | - Jacqueline C. M. Witteman
- Netherlands Consortium for Healthy Aging, Netherlands Genomics Initiative, Leiden, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tatiana Axenovich
- Institute of Cytology and Genetics, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Ben A. Oostra
- Centre for Medical Sytems Biology, Leiden, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Thomas Meitinger
- Institut for Human Genetics, Helmholtz-Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, München, Germany
- Munich Heart Alliance, Munich, Germany
| | - Andrew A. Hicks
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Alan F. Wright
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Ulf Gyllensten
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Harry Campbell
- Centre for Population Health Sciences, The University of Edinburgh Medical School, Edinburgh, United Kingdom
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
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7
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Zaboli G, Ameur A, Igl W, Johansson Å, Hayward C, Vitart V, Campbell S, Zgaga L, Polasek O, Schmitz G, van Duijn C, Oostra B, Pramstaller P, Hicks A, Meitinger T, Rudan I, Wright A, Wilson JF, Campbell H, Gyllensten U. Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits. Eur J Hum Genet 2011; 20:77-83. [PMID: 21811304 DOI: 10.1038/ejhg.2011.138] [Citation(s) in RCA: 10] [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: 01/29/2023] Open
Abstract
We have used targeted genomic sequencing of high-complexity DNA pools based on long-range PCR and deep DNA sequencing by the SOLiD technology. The method was used for sequencing of 286 kb from four chromosomal regions with quantitative trait loci (QTL) influencing blood plasma lipid and uric acid levels in DNA pools of 500 individuals from each of five European populations. The method shows very good precision in estimating allele frequencies as compared with individual genotyping of SNPs (r(2) = 0.95, P < 10(-16)). Validation shows that the method is able to identify novel SNPs and estimate their frequency in high-complexity DNA pools. In our five populations, 17% of all SNPs and 61% of structural variants are not available in the public databases. A large fraction of the novel variants show a limited geographic distribution, with 62% of the novel SNPs and 59% of novel structural variants being detected in only one of the populations. The large number of population-specific novel SNPs underscores the need for comprehensive sequencing of local populations in order to identify the causal variants of human traits.
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Affiliation(s)
- Ghazal Zaboli
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, SciLifeLab Uppsala, Uppsala University, Uppsala, Sweden
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8
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Obeidat M, Wain LV, Shrine N, Kalsheker N, Artigas MS, Repapi E, Burton PR, Johnson T, Ramasamy A, Zhao JH, Zhai G, Huffman JE, Vitart V, Albrecht E, Igl W, Hartikainen AL, Pouta A, Cadby G, Hui J, Palmer LJ, Hadley D, McArdle WL, Rudnicka AR, Barroso I, Loos RJF, Wareham NJ, Mangino M, Soranzo N, Spector TD, Gläser S, Homuth G, Völzke H, Deloukas P, Granell R, Henderson J, Grkovic I, Jankovic S, Zgaga L, Polašek O, Rudan I, Wright AF, Campbell H, Wild SH, Wilson JF, Heinrich J, Imboden M, Probst-Hensch NM, Gyllensten U, Johansson Å, Zaboli G, Mustelin L, Rantanen T, Surakka I, Kaprio J, Jarvelin MR, Hayward C, Evans DM, Koch B, Musk AW, Elliott P, Strachan DP, Tobin MD, Sayers I, Hall IP, Consortium S. A comprehensive evaluation of potential lung function associated genes in the SpiroMeta general population sample. PLoS One 2011; 6:e19382. [PMID: 21625484 PMCID: PMC3098839 DOI: 10.1371/journal.pone.0019382] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [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: 02/11/2011] [Accepted: 03/28/2011] [Indexed: 12/04/2022] Open
Abstract
RATIONALE Lung function measures are heritable traits that predict population morbidity and mortality and are essential for the diagnosis of chronic obstructive pulmonary disease (COPD). Variations in many genes have been reported to affect these traits, but attempts at replication have provided conflicting results. Recently, we undertook a meta-analysis of Genome Wide Association Study (GWAS) results for lung function measures in 20,288 individuals from the general population (the SpiroMeta consortium). OBJECTIVES To comprehensively analyse previously reported genetic associations with lung function measures, and to investigate whether single nucleotide polymorphisms (SNPs) in these genomic regions are associated with lung function in a large population sample. METHODS We analysed association for SNPs tagging 130 genes and 48 intergenic regions (+/-10 kb), after conducting a systematic review of the literature in the PubMed database for genetic association studies reporting lung function associations. RESULTS The analysis included 16,936 genotyped and imputed SNPs. No loci showed overall significant association for FEV(1) or FEV(1)/FVC traits using a carefully defined significance threshold of 1.3×10(-5). The most significant loci associated with FEV(1) include SNPs tagging MACROD2 (P = 6.81×10(-5)), CNTN5 (P = 4.37×10(-4)), and TRPV4 (P = 1.58×10(-3)). Among ever-smokers, SERPINA1 showed the most significant association with FEV(1) (P = 8.41×10(-5)), followed by PDE4D (P = 1.22×10(-4)). The strongest association with FEV(1)/FVC ratio was observed with ABCC1 (P = 4.38×10(-4)), and ESR1 (P = 5.42×10(-4)) among ever-smokers. CONCLUSIONS Polymorphisms spanning previously associated lung function genes did not show strong evidence for association with lung function measures in the SpiroMeta consortium population. Common SERPINA1 polymorphisms may affect FEV(1) among smokers in the general population.
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Affiliation(s)
- Ma'en Obeidat
- Nottingham Respiratory Biomedical Research Unit, Division of Therapeutics and Molecular Medicine, University Hospital of Nottingham, Nottingham, United Kingdom
| | - Louise V. Wain
- Departments of Health Sciences and Genetics, University of Leicester, Leicester, United Kingdom
| | - Nick Shrine
- Departments of Health Sciences and Genetics, University of Leicester, Leicester, United Kingdom
| | - Noor Kalsheker
- School of Molecular Medical Sciences and Centre for Genetics and Genomics, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Maria Soler Artigas
- Departments of Health Sciences and Genetics, University of Leicester, Leicester, United Kingdom
| | - Emmanouela Repapi
- Departments of Health Sciences and Genetics, University of Leicester, Leicester, United Kingdom
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Paul R. Burton
- Departments of Health Sciences and Genetics, University of Leicester, Leicester, United Kingdom
| | - Toby Johnson
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary, University of London, London, United Kingdom
| | - Adaikalavan Ramasamy
- Respiratory Epidemiology and Public Health Group, National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
| | - Jing Hua Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, Cambridge, United Kingdom
| | - Guangju Zhai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Jennifer E. Huffman
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, Scotland, United Kingdom
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, Scotland, United Kingdom
| | - Eva Albrecht
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Wilmar Igl
- Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Anna-Liisa Hartikainen
- Department of Clinical Sciences, Obstetrics and Gynecology, Institute of Clinical Medicine, University of Oulu, Oulu, Finland
| | - Anneli Pouta
- Department of Life Course and Services, National Institute for Health and Welfare, Oulu, Finland
| | - Gemma Cadby
- Ontario Institute for Cancer Research, Toronto, Canada
- Samuel Lunenfeld Research Institute, Toronto, Canada
| | - Jennie Hui
- Molecular Genetics, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- Busselton Population Medical Research Foundation, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- Schools of Population Health and Pathology and Laboratory Medicine, University of Western Australia, Crawley, Australia
| | - Lyle J. Palmer
- Ontario Institute for Cancer Research, Toronto, Canada
- Samuel Lunenfeld Research Institute, Toronto, Canada
| | - David Hadley
- Division of Community Health Sciences, St George's University of London, London, United Kingdom
- Pediatric Epidemiology Center, University of South Florida, Tampa, Florida, United States of America
| | - Wendy L. McArdle
- ALSPAC Laboratory, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Alicja R. Rudnicka
- Division of Community Health Sciences, St George's University of London, London, United Kingdom
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- University of Cambridge Metabolic Research Labs, Institute of Metabolic Science Addenbrooke's Hospital Cambridge, Cambridge, United Kingdom
| | - Ruth J. F. Loos
- MRC Epidemiology Unit, Institute of Metabolic Science, Cambridge, United Kingdom
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, Cambridge, United Kingdom
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Nicole Soranzo
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Sven Gläser
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University of Greifswald, Greifswald, Germany
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, SHIP/Clinical-Epidemiological Research, University of Greifswald, Greifswald, Germany
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Raquel Granell
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - John Henderson
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Ivica Grkovic
- Croatian Centre for Global Health, The University of Split Medical School, Split, Croatia
| | - Stipan Jankovic
- Croatian Centre for Global Health, The University of Split Medical School, Split, Croatia
| | - Lina Zgaga
- Andrija Stampar School of Public Health, Faculty of Medicine, University of Zagreb, Zagreb, Croatia
| | - Ozren Polašek
- Department of Public Health, University of Split, Split, Croatia
| | - Igor Rudan
- Croatian Centre for Global Health, The University of Split Medical School, Split, Croatia
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Alan F. Wright
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, Scotland, United Kingdom
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Sarah H. Wild
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - James F. Wilson
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Joachim Heinrich
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Nicole M. Probst-Hensch
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Ulf Gyllensten
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Åsa Johansson
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ghazal Zaboli
- Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Linda Mustelin
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Taina Rantanen
- Department of Health Sciences and Gerontology Research Centre, University of Jyväskylä, Jyväskylä, Finland
| | - Ida Surakka
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Jaakko Kaprio
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
- Department of Life Course and Services, National Institute for Health and Welfare, Oulu, Finland
- Institute of Health Sciences, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, Scotland, United Kingdom
| | - David M. Evans
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Beate Koch
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University of Greifswald, Greifswald, Germany
| | - Arthur William Musk
- Busselton Population Medical Research Foundation, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- Schools of Population Health and Medicine and Pharmacology, University of Western Australia, Crawley, Australia
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
- MRC-HPA Centre for Environment and Health, Imperial College London, London, United Kingdom
| | - David P. Strachan
- Division of Community Health Sciences, St George's University of London, London, United Kingdom
| | - Martin D. Tobin
- Departments of Health Sciences and Genetics, University of Leicester, Leicester, United Kingdom
| | - Ian Sayers
- Nottingham Respiratory Biomedical Research Unit, Division of Therapeutics and Molecular Medicine, University Hospital of Nottingham, Nottingham, United Kingdom
| | - Ian P. Hall
- Nottingham Respiratory Biomedical Research Unit, Division of Therapeutics and Molecular Medicine, University Hospital of Nottingham, Nottingham, United Kingdom
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Köttgen A, Pattaro C, Böger CA, Fuchsberger C, Olden M, Glazer NL, Parsa A, Gao X, Yang Q, Smith AV, O'Connell JR, Li M, Schmidt H, Tanaka T, Isaacs A, Ketkar S, Hwang SJ, Johnson AD, Dehghan A, Teumer A, Paré G, Atkinson EJ, Zeller T, Lohman K, Cornelis MC, Probst-Hensch NM, Kronenberg F, Tönjes A, Hayward C, Aspelund T, Eiriksdottir G, Launer LJ, Harris TB, Rampersaud E, Mitchell BD, Arking DE, Boerwinkle E, Struchalin M, Cavalieri M, Singleton A, Giallauria F, Metter J, de Boer IH, Haritunians T, Lumley T, Siscovick D, Psaty BM, Zillikens MC, Oostra BA, Feitosa M, Province M, de Andrade M, Turner ST, Schillert A, Ziegler A, Wild PS, Schnabel RB, Wilde S, Munzel TF, Leak TS, Illig T, Klopp N, Meisinger C, Wichmann HE, Koenig W, Zgaga L, Zemunik T, Kolcic I, Minelli C, Hu FB, Johansson A, Igl W, Zaboli G, Wild SH, Wright AF, Campbell H, Ellinghaus D, Schreiber S, Aulchenko YS, Felix JF, Rivadeneira F, Uitterlinden AG, Hofman A, Imboden M, Nitsch D, Brandstätter A, Kollerits B, Kedenko L, Mägi R, Stumvoll M, Kovacs P, Boban M, Campbell S, Endlich K, Völzke H, Kroemer HK, Nauck M, Völker U, Polasek O, Vitart V, Badola S, Parker AN, Ridker PM, Kardia SLR, Blankenberg S, Liu Y, Curhan GC, Franke A, Rochat T, Paulweber B, Prokopenko I, Wang W, Gudnason V, Shuldiner AR, Coresh J, Schmidt R, Ferrucci L, Shlipak MG, van Duijn CM, Borecki I, Krämer BK, Rudan I, Gyllensten U, Wilson JF, Witteman JC, Pramstaller PP, Rettig R, Hastie N, Chasman DI, Kao WH, Heid IM, Fox CS. New loci associated with kidney function and chronic kidney disease. Nat Genet 2010; 42:376-84. [PMID: 20383146 DOI: 10.1038/ng.568] [Citation(s) in RCA: 623] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 03/01/2010] [Indexed: 11/09/2022]
Abstract
Chronic kidney disease (CKD) is a significant public health problem, and recent genetic studies have identified common CKD susceptibility variants. The CKDGen consortium performed a meta-analysis of genome-wide association data in 67,093 individuals of European ancestry from 20 predominantly population-based studies in order to identify new susceptibility loci for reduced renal function as estimated by serum creatinine (eGFRcrea), serum cystatin c (eGFRcys) and CKD (eGFRcrea < 60 ml/min/1.73 m(2); n = 5,807 individuals with CKD (cases)). Follow-up of the 23 new genome-wide-significant loci (P < 5 x 10(-8)) in 22,982 replication samples identified 13 new loci affecting renal function and CKD (in or near LASS2, GCKR, ALMS1, TFDP2, DAB2, SLC34A1, VEGFA, PRKAG2, PIP5K1B, ATXN2, DACH1, UBE2Q2 and SLC7A9) and 7 loci suspected to affect creatinine production and secretion (CPS1, SLC22A2, TMEM60, WDR37, SLC6A13, WDR72 and BCAS3). These results further our understanding of the biologic mechanisms of kidney function by identifying loci that potentially influence nephrogenesis, podocyte function, angiogenesis, solute transport and metabolic functions of the kidney.
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Affiliation(s)
- Anna Köttgen
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland, USA
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10
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Repapi E, Sayers I, Wain LV, Burton PR, Johnson T, Obeidat M, Zhao JH, Ramasamy A, Zhai G, Vitart V, Huffman JE, Igl W, Albrecht E, Deloukas P, Henderson J, Granell R, McArdle WL, Rudnicka AR, Barroso I, Loos RJF, Wareham NJ, Mustelin L, Rantanen T, Surakka I, Imboden M, Wichmann HE, Grkovic I, Jankovic S, Zgaga L, Hartikainen AL, Peltonen L, Gyllensten U, Johansson A, Zaboli G, Campbell H, Wild SH, Wilson JF, Gläser S, Homuth G, Völzke H, Mangino M, Soranzo N, Spector TD, Polasek O, Rudan I, Wright AF, Heliövaara M, Ripatti S, Pouta A, Naluai AT, Olin AC, Torén K, Cooper MN, James AL, Palmer LJ, Hingorani AD, Wannamethee SG, Whincup PH, Smith GD, Ebrahim S, McKeever TM, Pavord ID, MacLeod AK, Morris AD, Porteous DJ, Cooper C, Dennison E, Shaheen S, Karrasch S, Schnabel E, Schulz H, Grallert H, Bouatia-Naji N, Delplanque J, Froguel P, Blakey JD, Britton JR, Morris RW, Holloway JW, Lawlor DA, Hui J, Nyberg F, Jarvelin MR, Jackson C, Kähönen M, Kaprio J, Probst-Hensch NM, Koch B, Hayward C, Evans DM, Elliott P, Strachan DP, Hall IP, Tobin MD. Genome-wide association study identifies five loci associated with lung function. Nat Genet 2010; 42:36-44. [PMID: 20010834 PMCID: PMC2862965 DOI: 10.1038/ng.501] [Citation(s) in RCA: 437] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Accepted: 11/10/2009] [Indexed: 12/18/2022]
Abstract
Pulmonary function measures are heritable traits that predict morbidity and mortality and define chronic obstructive pulmonary disease (COPD). We tested genome-wide association with forced expiratory volume in 1 s (FEV(1)) and the ratio of FEV(1) to forced vital capacity (FVC) in the SpiroMeta consortium (n = 20,288 individuals of European ancestry). We conducted a meta-analysis of top signals with data from direct genotyping (n < or = 32,184 additional individuals) and in silico summary association data from the CHARGE Consortium (n = 21,209) and the Health 2000 survey (n < or = 883). We confirmed the reported locus at 4q31 and identified associations with FEV(1) or FEV(1)/FVC and common variants at five additional loci: 2q35 in TNS1 (P = 1.11 x 10(-12)), 4q24 in GSTCD (2.18 x 10(-23)), 5q33 in HTR4 (P = 4.29 x 10(-9)), 6p21 in AGER (P = 3.07 x 10(-15)) and 15q23 in THSD4 (P = 7.24 x 10(-15)). mRNA analyses showed expression of TNS1, GSTCD, AGER, HTR4 and THSD4 in human lung tissue. These associations offer mechanistic insight into pulmonary function regulation and indicate potential targets for interventions to alleviate respiratory disease.
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Affiliation(s)
- Emmanouela Repapi
- Departments of Health Sciences and Genetics, Adrian Building, University of Leicester, Leicester, UK
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11
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Hicks AA, Pramstaller PP, Johansson Å, Vitart V, Rudan I, Ugocsai P, Aulchenko Y, Franklin CS, Liebisch G, Erdmann J, Jonasson I, Zorkoltseva IV, Pattaro C, Hayward C, Isaacs A, Hengstenberg C, Campbell S, Gnewuch C, Janssens AC, Kirichenko AV, König IR, Marroni F, Polasek O, Demirkan A, Kolcic I, Schwienbacher C, Igl W, Biloglav Z, Witteman JCM, Pichler I, Zaboli G, Axenovich TI, Peters A, Schreiber S, Wichmann HE, Schunkert H, Hastie N, Oostra BA, Wild SH, Meitinger T, Gyllensten U, van Duijn CM, Wilson JF, Wright A, Schmitz G, Campbell H. Genetic determinants of circulating sphingolipid concentrations in European populations. PLoS Genet 2009; 5:e1000672. [PMID: 19798445 PMCID: PMC2745562 DOI: 10.1371/journal.pgen.1000672] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 09/02/2009] [Indexed: 01/01/2023] Open
Abstract
Sphingolipids have essential roles as structural components of cell membranes and in cell signalling, and disruption of their metabolism causes several diseases, with diverse neurological, psychiatric, and metabolic consequences. Increasingly, variants within a few of the genes that encode enzymes involved in sphingolipid metabolism are being associated with complex disease phenotypes. Direct experimental evidence supports a role of specific sphingolipid species in several common complex chronic disease processes including atherosclerotic plaque formation, myocardial infarction (MI), cardiomyopathy, pancreatic beta-cell failure, insulin resistance, and type 2 diabetes mellitus. Therefore, sphingolipids represent novel and important intermediate phenotypes for genetic analysis, yet little is known about the major genetic variants that influence their circulating levels in the general population. We performed a genome-wide association study (GWAS) between 318,237 single-nucleotide polymorphisms (SNPs) and levels of circulating sphingomyelin (SM), dihydrosphingomyelin (Dih-SM), ceramide (Cer), and glucosylceramide (GluCer) single lipid species (33 traits); and 43 matched metabolite ratios measured in 4,400 subjects from five diverse European populations. Associated variants (32) in five genomic regions were identified with genome-wide significant corrected p-values ranging down to 9.08x10(-66). The strongest associations were observed in or near 7 genes functionally involved in ceramide biosynthesis and trafficking: SPTLC3, LASS4, SGPP1, ATP10D, and FADS1-3. Variants in 3 loci (ATP10D, FADS3, and SPTLC3) associate with MI in a series of three German MI studies. An additional 70 variants across 23 candidate genes involved in sphingolipid-metabolizing pathways also demonstrate association (p = 10(-4) or less). Circulating concentrations of several key components in sphingolipid metabolism are thus under strong genetic control, and variants in these loci can be tested for a role in the development of common cardiovascular, metabolic, neurological, and psychiatric diseases.
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Affiliation(s)
- Andrew A. Hicks
- Institute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Peter P. Pramstaller
- Institute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
- Department of Neurology, General Central Hospital, Bolzano, Italy
- Department of Neurology, University of Lübeck, Lübeck, Germany
- * E-mail: (PPP); (HC)
| | - Åsa Johansson
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Veronique Vitart
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh, United Kingdom
| | - Igor Rudan
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Croatian Centre for Global Health, Faculty of Medicine, University of Split, Split, Croatia
- Gen-info Ltd, Zagreb, Croatia
| | - Peter Ugocsai
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Yurii Aulchenko
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Gerhard Liebisch
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | | | - Inger Jonasson
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Cristian Pattaro
- Institute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Caroline Hayward
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh, United Kingdom
| | - Aaron Isaacs
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Christian Hengstenberg
- Klinik und Poliklinik für Innere Medizin II, Universität Regensburg, Regensburg, Germany
| | - Susan Campbell
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh, United Kingdom
| | - Carsten Gnewuch
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - A. CecileJ.W. Janssens
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Inke R. König
- Institut für Medizinische Biometrie und Statistik, University of Lübeck, Lübeck, Germany
| | - Fabio Marroni
- Institute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Ozren Polasek
- Gen-info Ltd, Zagreb, Croatia
- Andrija Stampar School of Public Health, Faculty of Medicine, University of Zagreb, Zagreb, Croatia
| | - Ayse Demirkan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ivana Kolcic
- Andrija Stampar School of Public Health, Faculty of Medicine, University of Zagreb, Zagreb, Croatia
| | - Christine Schwienbacher
- Institute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
- Department of Experimental and Diagnostic Medicine, University of Ferrara, Ferrara, Italy
| | - Wilmar Igl
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Zrinka Biloglav
- Andrija Stampar School of Public Health, Faculty of Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Irene Pichler
- Institute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Ghazal Zaboli
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Stefan Schreiber
- Institut für Klinische Molekularbiologie, Christian-Albrechts Universität, Kiel, Germany
| | - H.-Erich Wichmann
- Institute of Epidemiology, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Information Science, Biometry and Epidemiology, Chair of Epidemiology, LMU Munich, Germany
| | | | - Nick Hastie
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh, United Kingdom
| | - Ben A. Oostra
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sarah H. Wild
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Ulf Gyllensten
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Cornelia M. van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - James F. Wilson
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Alan Wright
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh, United Kingdom
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (PPP); (HC)
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Zaboli G, Jönsson EG, Gizatullin R, De Franciscis A, Asberg M, Leopardi R. Haplotype analysis confirms association of the serotonin transporter (5-HTT) gene with schizophrenia but not with major depression. Am J Med Genet B Neuropsychiatr Genet 2008; 147:301-7. [PMID: 17886257 DOI: 10.1002/ajmg.b.30597] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Serotonin (5-HT) has been implicated in the pathophysiology of several psychiatric disorders including major depressive disorder (MDD) and schizophrenia (SCZ). The serotonin transporter (5-HTT) is a major regulator of 5-HT function. 5-HTT gene polymorphic variants have been associated with both MDD and SCZ. A case-control design was used for candidate gene-disease association in 194 MDD patients, 155 schizophrenic psychosis patients, and 246 healthy controls, all North European Caucasians. Four polymorphisms were analyzed in terms of genotype, allele, and haplotype-based associations. Linkage disequilibrium (LD) analysis was also carried out. Bonferroni correction was used for multiple testing. Haplotype-based analyses showed significant associations between 5-HTT and SCZ but not MDD. No single locus associations were observed. In agreement with published meta-analysis our results indicate that 5-HTT associates with SCZ but not with MDD. It appears that risk for SCZ maps within a specific 5-HTT haplotype block.
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Affiliation(s)
- Ghazal Zaboli
- Department of Clinical Neuroscience, Psychiatry Section, Karolinska Institute and Hospital, Stockholm, Sweden
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13
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Gizatullin R, Zaboli G, Jönsson EG, Asberg M, Leopardi R. The tryptophan hydroxylase (TPH) 2 gene unlike TPH-1 exhibits no association with stress-induced depression. J Affect Disord 2008; 107:175-9. [PMID: 17692928 DOI: 10.1016/j.jad.2007.07.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 07/06/2007] [Accepted: 07/07/2007] [Indexed: 01/24/2023]
Abstract
BACKGROUND Serotonin (5-HT) has been implicated in the pathophysiology of several psychiatric disorders including major depression (MD). Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in the biosynthesis of serotonin (5-HT), and might be related to the pathogenesis of MD. Two isoforms are known, TPH-1 and TPH-2. Their association with MD is still debated. METHODS A case-control design was used for candidate gene-disease association in 194 patients with stress-induced MD, and 246 healthy controls, all North European Caucasians. Five TPH-2 polymorphisms were analyzed in terms of genotype, allele, and haplotype-based associations. RESULTS Neither single marker nor haplotype-based analyses showed significant associations between TPH-2 and MD. LIMITATIONS The interpretations are limited by the restricted population size. CONCLUSIONS There was no association between TPH-2 gene variants and MD in the same population that had shown a strong association with TPH-1. Hence, the results suggest that in this particular group of stress-induced depression patients TPH-1 appears to be more relevant to MD pathogenesis than TPH-2.
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Affiliation(s)
- Rinat Gizatullin
- Department of Clinical Neuroscience, Psychiatry Section, Karolinska University Hospital, SE-17176 Stockholm, Sweden
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14
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Zaboli G, Jönsson EG, Gizatullin R, Asberg M, Leopardi R. Tryptophan hydroxylase-1 gene variants associated with schizophrenia. Biol Psychiatry 2006; 60:563-9. [PMID: 16806098 DOI: 10.1016/j.biopsych.2006.03.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Revised: 03/16/2006] [Accepted: 03/22/2006] [Indexed: 11/16/2022]
Abstract
BACKGROUND Serotonin (5-HT) has been implicated in the pathophysiology of schizophrenia. Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in the biosynthesis of serotonin (5-HT), and as such it might be related to the pathogenesis of schizophrenia. Two isoforms are known, TPH-1 and TPH-2. TPH-1 association with schizophrenia is debated. METHODS A case-control design was employed for gene-disease association in 155 schizophrenic psychosis patients and 253 healthy controls, all North European Caucasians. Six single nucleotide polymorphisms (SNPs) with a haplotype block structure spanning over 23 kb of the total TPH-1 29 kb were analyzed. Linkage disequilibrium and haplotype analyses were performed. Bonferroni correction was used for multiple testing. RESULTS Single marker association analyses showed two SNPs significantly associated with schizophrenia. Several haplotypes were associated with the disease. A "sliding window" analysis attributed the strongest disease association to a haplotype configuration localized between the promoter region and intron 3. CONCLUSIONS Our data indicate that TPH-1 associates with schizophrenia. It appears that specific combinations of promoter variants vis-à-vis gene transcript variants contribute to genetic predisposition to the disease.
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Affiliation(s)
- Ghazal Zaboli
- Department of Clinical Neuroscience, Psychiatry Section, Karolinska Institute and Hospital, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden.
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15
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Zaboli G, Gizatullin R, Nilsonne A, Wilczek A, Jönsson EG, Ahnemark E, Asberg M, Leopardi R. Tryptophan hydroxylase-1 gene variants associate with a group of suicidal borderline women. Neuropsychopharmacology 2006; 31:1982-90. [PMID: 16495936 DOI: 10.1038/sj.npp.1301046] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alterations in the serotonin (5-HT) system have been related to impulsive aggression and suicidal behavior, common features of the borderline personality disorder (BPD). Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in 5-HT biosynthesis. Two isoforms are known, TPH-1 and TPH-2. TPH-1 has been correlated to various psychiatric and behavioral disorders by gene polymorphism association studies. We aimed to determine whether specific TPH-1 haplotypes associate with BPD. A case-control design was employed. The control group included 98 women without psychiatric history. In all, 95 patients were included, all Caucasian women with a BPD diagnosis who had attempted suicide at least twice during their lifetime. Exclusion criteria were: (i) substance dependence; (ii) dementia or other irreversible organic brain syndromes; (iii) psychotic disorders or major depressive illness with melancholic features; (iv) life-threatening eating disorders. Six single-nucleotide polymorphisms (SNPs) were found at significant linkage disequilibrium across 23 kb of the TPH-1 gene in both patients and controls, suggesting a haplotype block structure. While no individual SNP showed association, several haplotypes associated with the BPD group. In particular, one six-SNP haplotype was absent from the control group while representing about one-quarter of all haplotypes in the BPD group (corrected P<<10(-5)). A 'sliding window' analysis attributed the strongest disease association to haplotype configurations located between the gene promoter and intron 3. We conclude that TPH-1 associates with BPD in suicidal women. Our data support the expectation that haplotype analysis is superior to single locus analysis in gene-disease, case-control association studies.
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Affiliation(s)
- Ghazal Zaboli
- Psychiatry Section, Department of Clinical Neuroscience, Karolinska Institute and Hospital, Stockholm, Sweden.
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16
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Gizatullin R, Zaboli G, Jönsson EG, Asberg M, Leopardi R. Haplotype analysis reveals tryptophan hydroxylase (TPH) 1 gene variants associated with major depression. Biol Psychiatry 2006; 59:295-300. [PMID: 16165107 DOI: 10.1016/j.biopsych.2005.07.034] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2005] [Revised: 07/12/2005] [Accepted: 07/27/2005] [Indexed: 11/28/2022]
Abstract
BACKGROUND Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in the biosynthesis of serotonin (5-HT) and might be related to the pathogenesis of major depression (MD). Two isoforms are known, TPH-1 and TPH-2. Tryptophan hydroxylase-1 association with MD is still debated. METHODS A single nucleotide polymorphism (SNP) screening strategy was used to define TPH-1 haplotypes spanning over 23 kilobase (kb) of the 29 kb gene length. Genotyping was performed in 228 MD patients and 253 healthy control subjects. RESULTS Six SNPs were found at linkage disequilibrium in both patients and control subjects, suggesting a haplotype block structure. Single marker association analyses showed only one SNP significantly associated with MD. Several haplotypes were associated with MD. When all six locus haplotypes were divided into two groups, above or below a 5% threshold, the compound haplotype group below a 5% frequency resulted as associated with the disease (31.6% vs. 18.0% in control subjects, p < 10(-5)). A "sliding window" analysis attributed the strongest disease association to a haplotype configuration localized between introns 7 and 8 (p < 10(-5)). CONCLUSIONS Haplotype analysis indicates that TPH-1 associates with MD. The most common TPH-1 variants appear to carry no risk, while some of the less frequent variants might contribute to genetic predisposition to MD.
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Affiliation(s)
- Rinat Gizatullin
- Department of Clinical Neuroscience, Psychiatry Section, Karolinska Institute and Hospital, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
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