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Debette S, Ibrahim Verbaas CA, Bressler J, Schuur M, Smith A, Bis JC, Davies G, Wolf C, Gudnason V, Chibnik LB, Yang Q, deStefano AL, de Quervain DJF, Srikanth V, Lahti J, Grabe HJ, Smith JA, Priebe L, Yu L, Karbalai N, Hayward C, Wilson JF, Campbell H, Petrovic K, Fornage M, Chauhan G, Yeo R, Boxall R, Becker J, Stegle O, Mather KA, Chouraki V, Sun Q, Rose LM, Resnick S, Oldmeadow C, Kirin M, Wright AF, Jonsdottir MK, Au R, Becker A, Amin N, Nalls MA, Turner ST, Kardia SLR, Oostra B, Windham G, Coker LH, Zhao W, Knopman DS, Heiss G, Griswold ME, Gottesman RF, Vitart V, Hastie ND, Zgaga L, Rudan I, Polasek O, Holliday EG, Schofield P, Choi SH, Tanaka T, An Y, Perry RT, Kennedy RE, Sale MM, Wang J, Wadley VG, Liewald DC, Ridker PM, Gow AJ, Pattie A, Starr JM, Porteous D, Liu X, Thomson R, Armstrong NJ, Eiriksdottir G, Assareh AA, Kochan NA, Widen E, Palotie A, Hsieh YC, Eriksson JG, Vogler C, van Swieten JC, Shulman JM, Beiser A, Rotter J, Schmidt CO, Hoffmann W, Nöthen MM, Ferrucci L, Attia J, Uitterlinden AG, Amouyel P, Dartigues JF, Amieva H, Räikkönen K, Garcia M, Wolf PA, Hofman A, Longstreth WT, Psaty BM, Boerwinkle E, DeJager PL, Sachdev PS, Schmidt R, Breteler MMB, Teumer A, Lopez OL, Cichon S, Chasman DI, Grodstein F, Müller-Myhsok B, Tzourio C, Papassotiropoulos A, Bennett DA, Ikram MA, Deary IJ, van Duijn CM, Launer L, Fitzpatrick AL, Seshadri S, Mosley TH. Genome-wide studies of verbal declarative memory in nondemented older people: the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium. Biol Psychiatry 2015; 77:749-63. [PMID: 25648963 PMCID: PMC4513651 DOI: 10.1016/j.biopsych.2014.08.027] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 08/23/2014] [Accepted: 08/25/2014] [Indexed: 01/06/2023]
Abstract
BACKGROUND Memory performance in older persons can reflect genetic influences on cognitive function and dementing processes. We aimed to identify genetic contributions to verbal declarative memory in a community setting. METHODS We conducted genome-wide association studies for paragraph or word list delayed recall in 19 cohorts from the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium, comprising 29,076 dementia- and stroke-free individuals of European descent, aged ≥45 years. Replication of suggestive associations (p < 5 × 10(-6)) was sought in 10,617 participants of European descent, 3811 African-Americans, and 1561 young adults. RESULTS rs4420638, near APOE, was associated with poorer delayed recall performance in discovery (p = 5.57 × 10(-10)) and replication cohorts (p = 5.65 × 10(-8)). This association was stronger for paragraph than word list delayed recall and in the oldest persons. Two associations with specific tests, in subsets of the total sample, reached genome-wide significance in combined analyses of discovery and replication (rs11074779 [HS3ST4], p = 3.11 × 10(-8), and rs6813517 [SPOCK3], p = 2.58 × 10(-8)) near genes involved in immune response. A genetic score combining 58 independent suggestive memory risk variants was associated with increasing Alzheimer disease pathology in 725 autopsy samples. Association of memory risk loci with gene expression in 138 human hippocampus samples showed cis-associations with WDR48 and CLDN5, both related to ubiquitin metabolism. CONCLUSIONS This largest study to date exploring the genetics of memory function in ~40,000 older individuals revealed genome-wide associations and suggested an involvement of immune and ubiquitin pathways.
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Affiliation(s)
- Stéphanie Debette
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts; Institut National de la Santé et de la Recherche Médicale, Epidemiology, University of Bordeaux; Department of Neurology, University Hospital of Bordeaux, Bordeaux, France.
| | - Carla A Ibrahim Verbaas
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center University Medical Center, Rotterdam, The Netherlands; Department of Neurology, Erasmus Medical Center University Medical Center, Rotterdam, The Netherlands
| | - Jan Bressler
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas
| | - Maaike Schuur
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center University Medical Center, Rotterdam, The Netherlands; Department of Neurology, Erasmus Medical Center University Medical Center, Rotterdam, The Netherlands
| | - Albert Smith
- Icelandic Heart Association, Kopavogur; Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh; Department of Psychology, The University of Edinburgh; Medical Genetics Section, Molecular Medicine Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | | | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur; Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Lori B Chibnik
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Boston
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston; The National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, Massachusetts
| | - Anita L deStefano
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts; Department of Biostatistics, Boston University School of Public Health, Boston; The National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, Massachusetts
| | - Dominique J F de Quervain
- Psychiatric University Clinics and Department of Psychology, Division of Cognitive Neuroscience, University of Basel, Basel, Switzerland
| | - Velandai Srikanth
- Stroke and Ageing Research Centre, Southern Clinical School, Department of Medicine, Monash University, Melbourne; Menzies Research Institute Tasmania, University of Tasmania, Hobart, Australia
| | - Jari Lahti
- Institute of Behavioural Sciences, University of Helsinki; Folkhälsan Research Centre, Helsinki, Finland
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, HELIOS-Hospital Stralsund, Stralsund; German Center for Neurodegenerative Diseases, Site Rostock/ Greifswald, Rostock, Germany
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan
| | - Lutz Priebe
- Institute of Human Genetics, Universitätsklinikum Bonn, Bonn, Germany
| | - Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois
| | | | | | - James F Wilson
- Institute of Genetics and Molecular Medicine, University of Edinburgh, United Kingdom, Centre for Population Health Sciences, University of Edinburgh, United Kingdom
| | - Harry Campbell
- Division of General Neurology, Department of Neurology, Medical University and General Hospital of Graz, Austria
| | - Katja Petrovic
- Division of General Neurology, Department of Neurology, Medical University and General Hospital of Graz, Austria
| | - Myriam Fornage
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas; Institute of Molecular Medicine, University of Texas-Houston Health Science Center, Houston, Texas
| | - Ganesh Chauhan
- Institut National de la Santé et de la Recherche Médicale, Epidemiology, University of Bordeaux
| | - Robin Yeo
- Institut National de la Santé et de la Recherche Médicale, Epidemiology, University of Bordeaux
| | - Ruth Boxall
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh
| | - James Becker
- Departments of Neurology and Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Psychology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Oliver Stegle
- Max Planck Institute for Intelligent Systems, Tübingen, Germany; Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales Medicine, University of New South Wales, Sydney, Australia
| | - Vincent Chouraki
- Institut National de la Santé et de la Recherche Médicale Unit 744, Institut Pasteur de Lille, and Université Lille Nord de France, Lille, France
| | - Qi Sun
- Department of Nutrition, Harvard School of Public Health; Channing Division of Network Medicine, Department of Medicine, Brigham and Women׳s Hospital and Harvard Medical School; Harvard Medical School, Brigham and Women׳s Hospital, Boston, Massachusetts
| | - Lynda M Rose
- Division of Preventive Medicine, Brigham and Women׳s Hospital, Boston, Massachusetts
| | - Susan Resnick
- Brain Aging and Behavior Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - Christopher Oldmeadow
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine, Newcastle, Australia; Public Health, Faculty of Health, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia
| | - Mirna Kirin
- Institute of Genetics and Molecular Medicine, University of Edinburgh, United Kingdom, Centre for Population Health Sciences, University of Edinburgh, United Kingdom
| | - Alan F Wright
- Institute of Genetics and Molecular Medicine, University of Edinburgh, United Kingdom, Centre for Population Health Sciences, University of Edinburgh, United Kingdom
| | | | - Rhoda Au
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts; The National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, Massachusetts
| | - Albert Becker
- Institute of Neuropathology, Universitätsklinikum Bonn, Bonn, Germany
| | - Najaf Amin
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center University Medical Center, Rotterdam, The Netherlands
| | - Mike A Nalls
- Molecular Genetics Section , Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - Stephen T Turner
- Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan
| | - Ben Oostra
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center University Medical Center, Rotterdam, The Netherlands; Department of Clinical Genetics, Erasmus Medical Center University Medical Center, Rotterdam, The Netherlands
| | - Gwen Windham
- Department of Medicine, Division of Geriatrics, University of Mississippi Medical Center, Jackson, Mississippi
| | - Laura H Coker
- Division of Public Health Sciences and Neurology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Wei Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan
| | | | - Gerardo Heiss
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michael E Griswold
- Center of Biostatistics and Bioinformatics, University of Mississippi Medical Center, Jackson, Mississippi
| | - Rebecca F Gottesman
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | - Lina Zgaga
- Medical Research Council Human Genetics Unit
| | - Igor Rudan
- Institute of Genetics and Molecular Medicine, University of Edinburgh, United Kingdom, Centre for Population Health Sciences, University of Edinburgh, United Kingdom
| | - Ozren Polasek
- Department of Public Health, Faculty of Medicine, University of Split, Split, Croatia
| | - Elizabeth G Holliday
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine, Newcastle, Australia
| | - Peter Schofield
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine, Newcastle, Australia; Department of Medicine, John Hunter Hospital, Newcastle, Australia
| | - Seung Hoan Choi
- Department of Biostatistics, Boston University School of Public Health, Boston
| | - Toshiko Tanaka
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - Yang An
- Brain Aging and Behavior Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - Rodney T Perry
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Richard E Kennedy
- Division of Gerontology, Geriatrics, and Palliative Care, University of Alabama at Birmingham, Birmingham, Alabama
| | - Michèle M Sale
- Center for Public Health Genomics, Department of Medicine, Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia
| | - Jing Wang
- Department of Biostatistics, Boston University School of Public Health, Boston
| | - Virginia G Wadley
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - David C Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh; Department of Psychology, The University of Edinburgh
| | - Paul M Ridker
- Harvard Medical School, Brigham and Women׳s Hospital, Boston, Massachusetts; Division of Preventive Medicine, Brigham and Women׳s Hospital, Boston, Massachusetts
| | - Alan J Gow
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh; Department of Psychology, The University of Edinburgh
| | - Alison Pattie
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh; Alzheimer Scotland Dementia Research Centre, The University of Edinburgh, Edinburgh, United Kingdom
| | - David Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh; Medical Genetics Section, Molecular Medicine Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Xuan Liu
- Department of Biostatistics, Boston University School of Public Health, Boston
| | - Russell Thomson
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, Australia
| | - Nicola J Armstrong
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales Medicine, University of New South Wales, Sydney, Australia; Cancer Research Program, Garvan Institute of Medical Research, Darlinghurst; School of Mathematics & Statistics and Prince of Wales Clinical School, University of New South Wales, Sydney
| | | | - Arezoo A Assareh
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales Medicine, University of New South Wales, Sydney, Australia; Neuroscience Research Australia and Primary Dementia Collaborative Research Centre-Assessment and Better Care, University of New South Wales, Sydney
| | - Nicole A Kochan
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales Medicine, University of New South Wales, Sydney, Australia; Neuropsychiatric Institute, Prince of Wales Hospital, Randwick New South Wales, Australia
| | - Elisabeth Widen
- Institute for Molecular Medicine Finland, University of Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, University of Helsinki, Finland; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; Department of Medical Genetics, University of Helsinki and University Central Hospital, Helsinki, Finland
| | - Yi-Chen Hsieh
- Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Johan G Eriksson
- Folkhälsan Research Centre, Helsinki, Finland; National Institute for Health and Welfare, Helsinki, Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Helsinki University Central Hospital, Unit of General Practice, Helsinki, Vasa Central Hospital, Vasa, Finland
| | - Christian Vogler
- Psychiatric University Clinics and Department of Psychology, Division of Molecular Neuroscience, University of Basel, Basel, Switzerland
| | - John C van Swieten
- Department of Neurology, Erasmus Medical Center University Medical Center, Rotterdam, The Netherlands
| | - Joshua M Shulman
- Departments of Neurology and Molecular and Human Genetics, Baylor College of Medicine and The Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas
| | - Alexa Beiser
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts; Department of Biostatistics, Boston University School of Public Health, Boston; The National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, Massachusetts
| | - Jerome Rotter
- Institute for Translational Genomics and Populaton Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, California
| | | | - Wolfgang Hoffmann
- German Center for Neurodegenerative Diseases, Site Rostock/ Greifswald, Rostock, Germany; Section Epidemiology of Health Care and Community Health, Greifswald
| | - Markus M Nöthen
- Institute of Human Genetics, Department of Genomics, Life & Brain Research Center, University of Bonn, Bonn; German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - John Attia
- Centre for Clinical Epidemiology and Biostatistics, School of Medicine, Newcastle, Australia; Public Health, Faculty of Health, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia; Department of Medicine, John Hunter Hospital, Newcastle, Australia
| | - Andre G Uitterlinden
- Netherlands Consortium for Healthy Ageing, Leiden, the Netherlands; Department of Internal Medicine, Erasmus Medical Center University Medical Center, Rotterdam, the Netherlands
| | - Philippe Amouyel
- Institut National de la Santé et de la Recherche Médicale Unit 744, Institut Pasteur de Lille, and Université Lille Nord de France, Lille, France; Centre Hospitalier Régional Universitaire de Lille, Lille
| | - Jean-François Dartigues
- Institut National de la Santé et de la Recherche Médicale, Bordeaux University, Talence, France
| | - Hélène Amieva
- Institut National de la Santé et de la Recherche Médicale, Bordeaux University, Talence, France
| | | | - Melissa Garcia
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, Maryland
| | - Philip A Wolf
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts; The National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, Massachusetts
| | - Albert Hofman
- Netherlands Consortium for Healthy Ageing, Leiden, the Netherlands; Department of Epidemiology, Erasmus Medical Center University Medical Center, Rotterdam, The Netherlands
| | - W T Longstreth
- Departments of Neurology, University of Washington; Epidemiology, University of Washington
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington; Epidemiology, University of Washington; Health Services, University of Washington; Group Health Research Institute, Group Health Cooperative, Seattle, Washington
| | - Eric Boerwinkle
- Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, University of Texas Health Science Center at Houston, Houston, Texas
| | - Philip L DeJager
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Boston
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales Medicine, University of New South Wales, Sydney, Australia; Neuropsychiatric Institute, Prince of Wales Hospital, Randwick New South Wales, Australia
| | - Reinhold Schmidt
- Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, Austria
| | - Monique M B Breteler
- German Center for Neurodegenerative Diseases, Site Rostock/ Greifswald, Rostock, Germany; Netherlands Consortium for Healthy Ageing, Leiden, the Netherlands; Department of Epidemiology, Erasmus Medical Center University Medical Center, Rotterdam, The Netherlands; Population Health Sciences, University of Bonn, Bonn, Germany; Department of Epidemiology, Harvard School of Public Health, Harvard University, Boston, Massachusetts
| | - Alexander Teumer
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Oscar L Lopez
- Departments of Neurology and Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; The Alzheimer׳s Disease Research Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Sven Cichon
- Institute of Human Genetics, Universitätsklinikum Bonn, Bonn, Germany; Institute of Neuroscience and Medicine, Research Center Julich, Julich, Germany; Division of Medical Genetics, Department of Biomedicine, University of Basel, Switzerland
| | - Daniel I Chasman
- Harvard Medical School, Brigham and Women׳s Hospital, Boston, Massachusetts; Division of Preventive Medicine, Brigham and Women׳s Hospital, Boston, Massachusetts
| | - Francine Grodstein
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women׳s Hospital and Harvard Medical School; Department of Epidemiology, Harvard School of Public Health, Harvard University, Boston, Massachusetts
| | - Bertram Müller-Myhsok
- Max Planck Institute of Psychiatry, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Christophe Tzourio
- Institut National de la Santé et de la Recherche Médicale, Epidemiology, University of Bordeaux; University Bordeaux Segalen, Bordeaux, France
| | - Andreas Papassotiropoulos
- Psychiatric University Clinics and Department of Psychology, Division of Molecular Neuroscience, University of Basel, Basel, Switzerland; Department Biozentrum, Life Sciences Training Facility, Basel, Switzerland
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois
| | - M Arfan Ikram
- Netherlands Consortium for Healthy Ageing, Leiden, the Netherlands; Department of Epidemiology, Erasmus Medical Center University Medical Center, Rotterdam, The Netherlands; Department of Radiology, Erasmus Medical Center University Medical Center, Rotterdam, The Netherlands
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh; Department of Psychology, The University of Edinburgh
| | - Cornelia M van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center University Medical Center, Rotterdam, The Netherlands; Netherlands Consortium for Healthy Ageing, Leiden, the Netherlands; Center for Medical Systems Biology, Netherlands Genomics Initiative, Leiden University Medical Center, Leiden, The Netherlands
| | - Lenore Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, Maryland
| | | | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts; Department of Biostatistics, Boston University School of Public Health, Boston; The National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, Massachusetts
| | - Thomas H Mosley
- Department of Medicine and Neurology, University of Mississippi Medical Center, Jackson, Mississippi
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Zhang Y, Bonnan A, Bony G, Ferezou I, Pietropaolo S, Ginger M, Sans N, Rossier J, Oostra B, LeMasson G, Frick A. Dendritic channelopathies contribute to neocortical and sensory hyperexcitability in Fmr1(-/y) mice. Nat Neurosci 2014; 17:1701-9. [PMID: 25383903 DOI: 10.1038/nn.3864] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 10/14/2014] [Indexed: 12/14/2022]
Abstract
Hypersensitivity in response to sensory stimuli and neocortical hyperexcitability are prominent features of Fragile X Syndrome (FXS) and autism spectrum disorders, but little is known about the dendritic mechanisms underlying these phenomena. We found that the primary somatosensory neocortex (S1) was hyperexcited in response to tactile sensory stimulation in Fmr1(-/y) mice. This correlated with neuronal and dendritic hyperexcitability of S1 pyramidal neurons, which affect all major aspects of neuronal computation, from the integration of synaptic input to the generation of action potential output. Using dendritic electrophysiological recordings, calcium imaging, pharmacology, biochemistry and a computer model, we found that this defect was, at least in part, attributable to the reduction and dysfunction of dendritic h- and BKCa channels. We pharmacologically rescued several core hyperexcitability phenomena by targeting BKCa channels. Our results provide strong evidence pointing to the utility of BKCa channel openers for the treatment of the sensory hypersensitivity aspects of FXS.
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Affiliation(s)
- Yu Zhang
- 1] INSERM, Neurocentre Magendie, Physiopathologie de la plasticité neuronale, U862, Bordeaux, France. [2] University of Bordeaux, Neurocentre Magendie, Physiopathologie de la plasticité neuronale, U862, Bordeaux, France
| | - Audrey Bonnan
- 1] INSERM, Neurocentre Magendie, Physiopathologie de la plasticité neuronale, U862, Bordeaux, France. [2] University of Bordeaux, Neurocentre Magendie, Physiopathologie de la plasticité neuronale, U862, Bordeaux, France
| | - Guillaume Bony
- 1] INSERM, Neurocentre Magendie, Physiopathologie de la plasticité neuronale, U862, Bordeaux, France. [2] University of Bordeaux, Neurocentre Magendie, Physiopathologie de la plasticité neuronale, U862, Bordeaux, France
| | - Isabelle Ferezou
- Laboratoire de Neurobiologie, ESPCI ParisTech CNRS UMR 7637, Paris, France
| | - Susanna Pietropaolo
- 1] University of Bordeaux, INCIA, Talence, France. [2] CNRS, INCIA, UMR 5287, Talence, France
| | - Melanie Ginger
- 1] INSERM, Neurocentre Magendie, Physiopathologie de la plasticité neuronale, U862, Bordeaux, France. [2] University of Bordeaux, Neurocentre Magendie, Physiopathologie de la plasticité neuronale, U862, Bordeaux, France
| | - Nathalie Sans
- 1] INSERM, Neurocentre Magendie, Physiopathologie de la plasticité neuronale, U862, Bordeaux, France. [2] University of Bordeaux, Neurocentre Magendie, Physiopathologie de la plasticité neuronale, U862, Bordeaux, France
| | - Jean Rossier
- Laboratoire de Neurobiologie, ESPCI ParisTech CNRS UMR 7637, Paris, France
| | - Ben Oostra
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands
| | - Gwen LeMasson
- 1] INSERM, Neurocentre Magendie, Physiopathologie de la plasticité neuronale, U862, Bordeaux, France. [2] University of Bordeaux, Neurocentre Magendie, Physiopathologie de la plasticité neuronale, U862, Bordeaux, France
| | - Andreas Frick
- 1] INSERM, Neurocentre Magendie, Physiopathologie de la plasticité neuronale, U862, Bordeaux, France. [2] University of Bordeaux, Neurocentre Magendie, Physiopathologie de la plasticité neuronale, U862, Bordeaux, France
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Boomsma DI, Wijmenga C, Slagboom EP, Swertz MA, Karssen LC, Abdellaoui A, Ye K, Guryev V, Vermaat M, van Dijk F, Francioli LC, Hottenga JJ, Laros JFJ, Li Q, Li Y, Cao H, Chen R, Du Y, Li N, Cao S, van Setten J, Menelaou A, Pulit SL, Hehir-Kwa JY, Beekman M, Elbers CC, Byelas H, de Craen AJM, Deelen P, Dijkstra M, den Dunnen JT, de Knijff P, Houwing-Duistermaat J, Koval V, Estrada K, Hofman A, Kanterakis A, Enckevort DV, Mai H, Kattenberg M, van Leeuwen EM, Neerincx PBT, Oostra B, Rivadeneira F, Suchiman EHD, Uitterlinden AG, Willemsen G, Wolffenbuttel BH, Wang J, de Bakker PIW, van Ommen GJ, van Duijn CM. The Genome of the Netherlands: design, and project goals. Eur J Hum Genet 2014; 22:221-7. [PMID: 23714750 PMCID: PMC3895638 DOI: 10.1038/ejhg.2013.118] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 02/28/2013] [Accepted: 03/24/2013] [Indexed: 11/09/2022] Open
Abstract
Within the Netherlands a national network of biobanks has been established (Biobanking and Biomolecular Research Infrastructure-Netherlands (BBMRI-NL)) as a national node of the European BBMRI. One of the aims of BBMRI-NL is to enrich biobanks with different types of molecular and phenotype data. Here, we describe the Genome of the Netherlands (GoNL), one of the projects within BBMRI-NL. GoNL is a whole-genome-sequencing project in a representative sample consisting of 250 trio-families from all provinces in the Netherlands, which aims to characterize DNA sequence variation in the Dutch population. The parent-offspring trios include adult individuals ranging in age from 19 to 87 years (mean=53 years; SD=16 years) from birth cohorts 1910-1994. Sequencing was done on blood-derived DNA from uncultured cells and accomplished coverage was 14-15x. The family-based design represents a unique resource to assess the frequency of regional variants, accurately reconstruct haplotypes by family-based phasing, characterize short indels and complex structural variants, and establish the rate of de novo mutational events. GoNL will also serve as a reference panel for imputation in the available genome-wide association studies in Dutch and other cohorts to refine association signals and uncover population-specific variants. GoNL will create a catalog of human genetic variation in this sample that is uniquely characterized with respect to micro-geographic location and a wide range of phenotypes. The resource will be made available to the research and medical community to guide the interpretation of sequencing projects. The present paper summarizes the global characteristics of the project.
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Affiliation(s)
- Dorret I Boomsma
- Department of Biological Psychology, VU University Amsterdam, Netherlands Twin Register, Amsterdam, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Eline P Slagboom
- Molecular Epidemiology Section, Leiden University Medical Center, Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - Morris A Swertz
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Lennart C Karssen
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Abdel Abdellaoui
- Department of Biological Psychology, VU University Amsterdam, Netherlands Twin Register, Amsterdam, The Netherlands
| | - Kai Ye
- Molecular Epidemiology Section, Leiden University Medical Center, Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Martijn Vermaat
- Netherlands Bioinformatics Centre, Nijmegen, The Netherlands
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Freerk van Dijk
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Laurent C Francioli
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, VU University Amsterdam, Netherlands Twin Register, Amsterdam, The Netherlands
| | - Jeroen F J Laros
- Netherlands Bioinformatics Centre, Nijmegen, The Netherlands
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | | | | | | | - Ning Li
- BGI-Europe, Copenhagen, Denmark
| | | | - Jessica van Setten
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Androniki Menelaou
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sara L Pulit
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jayne Y Hehir-Kwa
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Marian Beekman
- Department of Gerontology and Geriatrics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Clara C Elbers
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Heorhiy Byelas
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Anton J M de Craen
- Department of Gerontology and Geriatrics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Patrick Deelen
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Martijn Dijkstra
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Johan T den Dunnen
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter de Knijff
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeanine Houwing-Duistermaat
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Vyacheslav Koval
- Erasmus Medical Centre, Genetic Laboratory Internal Medicine, Rotterdam, The Netherlands
| | - Karol Estrada
- Erasmus Medical Centre, Genetic Laboratory Internal Medicine, Rotterdam, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Alexandros Kanterakis
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | | | - Hailiang Mai
- Netherlands Bioinformatics Centre, Nijmegen, The Netherlands
| | - Mathijs Kattenberg
- Department of Biological Psychology, VU University Amsterdam, Netherlands Twin Register, Amsterdam, The Netherlands
| | | | - Pieter B T Neerincx
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Ben Oostra
- Department of Clinical Genetics, Erasmus University Medical School, Rotterdam, The Netherlands
| | - Fernanodo Rivadeneira
- Erasmus Medical Centre, Genetic Laboratory Internal Medicine, Rotterdam, The Netherlands
| | - Eka H D Suchiman
- Molecular Epidemiology Section, Leiden University Medical Center, Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands
| | - Andre G Uitterlinden
- Erasmus Medical Centre, Genetic Laboratory Internal Medicine, Rotterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, Netherlands Twin Register, Amsterdam, The Netherlands
| | - Bruce H Wolffenbuttel
- LifeLines Cohort Study & Department of Endocrinology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Paul I W de Bakker
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gert-Jan van Ommen
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
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Iglesias AI, Springelkamp H, van der Linde H, Severijnen LA, Amin N, Oostra B, Kockx CEM, van den Hout MCGN, van IJcken WFJ, Hofman A, Uitterlinden AG, Verdijk RM, Klaver CCW, Willemsen R, van Duijn CM. Exome sequencing and functional analyses suggest that SIX6 is a gene involved in an altered proliferation–differentiation balance early in life and optic nerve degeneration at old age. Hum Mol Genet 2013; 23:1320-32. [DOI: 10.1093/hmg/ddt522] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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Fernández-Rhodes L, Demerath EW, Cousminer DL, Tao R, Dreyfus JG, Esko T, Smith AV, Gudnason V, Harris TB, Launer L, McArdle PF, Yerges-Armstrong LM, Elks CE, Strachan DP, Kutalik Z, Vollenweider P, Feenstra B, Boyd HA, Metspalu A, Mihailov E, Broer L, Zillikens MC, Oostra B, van Duijn CM, Lunetta KL, Perry JRB, Murray A, Koller DL, Lai D, Corre T, Toniolo D, Albrecht E, Stöckl D, Grallert H, Gieger C, Hayward C, Polasek O, Rudan I, Wilson JF, He C, Kraft P, Hu FB, Hunter DJ, Hottenga JJ, Willemsen G, Boomsma DI, Byrne EM, Martin NG, Montgomery GW, Warrington NM, Pennell CE, Stolk L, Visser JA, Hofman A, Uitterlinden AG, Rivadeneira F, Lin P, Fisher SL, Bierut LJ, Crisponi L, Porcu E, Mangino M, Zhai G, Spector TD, Buring JE, Rose LM, Ridker PM, Poole C, Hirschhorn JN, Murabito JM, Chasman DI, Widen E, North KE, Ong KK, Franceschini N. Association of adiposity genetic variants with menarche timing in 92,105 women of European descent. Am J Epidemiol 2013; 178:451-60. [PMID: 23558354 DOI: 10.1093/aje/kws473] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Obesity is of global health concern. There are well-described inverse relationships between female pubertal timing and obesity. Recent genome-wide association studies of age at menarche identified several obesity-related variants. Using data from the ReproGen Consortium, we employed meta-analytical techniques to estimate the associations of 95 a priori and recently identified obesity-related (body mass index (weight (kg)/height (m)(2)), waist circumference, and waist:hip ratio) single-nucleotide polymorphisms (SNPs) with age at menarche in 92,116 women of European descent from 38 studies (1970-2010), in order to estimate associations between genetic variants associated with central or overall adiposity and pubertal timing in girls. Investigators in each study performed a separate analysis of associations between the selected SNPs and age at menarche (ages 9-17 years) using linear regression models and adjusting for birth year, site (as appropriate), and population stratification. Heterogeneity of effect-measure estimates was investigated using meta-regression. Six novel associations of body mass index loci with age at menarche were identified, and 11 adiposity loci previously reported to be associated with age at menarche were confirmed, but none of the central adiposity variants individually showed significant associations. These findings suggest complex genetic relationships between menarche and overall obesity, and to a lesser extent central obesity, in normal processes of growth and development.
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Affiliation(s)
- Lindsay Fernández-Rhodes
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, 137 East Franklin Street, Suite 306, Campus Box 8050, Chapel Hill, NC 27514-8050, USA.
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6
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Sun Y, Almomani R, Breedveld GJ, Santen GWE, Aten E, Lefeber DJ, Hoff JI, Brusse E, Verheijen FW, Verdijk RM, Kriek M, Oostra B, Breuning MH, Losekoot M, den Dunnen JT, van de Warrenburg BP, Maat-Kievit AJA. Autosomal recessive spinocerebellar ataxia 7 (SCAR7) is caused by variants in TPP1, the gene involved in classic late-infantile neuronal ceroid lipofuscinosis 2 disease (CLN2 disease). Hum Mutat 2013; 34:706-13. [PMID: 23418007 DOI: 10.1002/humu.22292] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 01/31/2013] [Indexed: 01/15/2023]
Abstract
Spinocerebellar ataxias are phenotypically, neuropathologically, and genetically heterogeneous. The locus of autosomal recessive spinocerebellar ataxia type 7 (SCAR7) was previously linked to chromosome band 11p15. We have identified TPP1 as the causative gene for SCAR7 by exome sequencing. A missense and a splice site variant in TPP1, cosegregating with the disease, were found in a previously described SCAR7 family and also in another patient with a SCAR7 phenotype. TPP1, encoding the tripeptidyl-peptidase 1 enzyme, is known as the causative gene for late infantile neuronal ceroid lipofuscinosis disease 2 (CLN2 disease). CLN2 disease is characterized by epilepsy, loss of vision, ataxia, and a rapidly progressive course, leading to early death. SCAR7 patients showed ataxia and low activity of tripeptidyl-peptidase 1, but no ophthalmologic abnormalities or epilepsy. Also, the slowly progressive evolution of the disease until old age and absence of ultra structural curvilinear profiles is different from the known CLN2 phenotypes. Our findings now expand the phenotypes related to TPP1-variants to SCAR7. In spite of the limited sample size and measurements, a putative genotype-phenotype correlation may be drawn: we hypothesize that loss of function variants abolishing TPP1 enzyme activity lead to CLN2 disease, whereas variants that diminish TPP1 enzyme activity lead to SCAR7.
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Affiliation(s)
- Yu Sun
- Center for Human and Clinical Genetics, Leiden University Medical Center, The Netherlands
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7
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Peters MJ, Broer L, Willemen HLDM, Eiriksdottir G, Hocking LJ, Holliday KL, Horan MA, Meulenbelt I, Neogi T, Popham M, Schmidt CO, Soni A, Valdes AM, Amin N, Dennison EM, Eijkelkamp N, Harris TB, Hart DJ, Hofman A, Huygen FJPM, Jameson KA, Jones GT, Launer LJ, Kerkhof HJM, de Kruijf M, McBeth J, Kloppenburg M, Ollier WE, Oostra B, Payton A, Rivadeneira F, Smith BH, Smith AV, Stolk L, Teumer A, Thomson W, Uitterlinden AG, Wang K, van Wingerden SH, Arden NK, Cooper C, Felson D, Gudnason V, Macfarlane GJ, Pendleton N, Slagboom PE, Spector TD, Völzke H, Kavelaars A, van Duijn CM, Williams FMK, van Meurs JBJ. Genome-wide association study meta-analysis of chronic widespread pain: evidence for involvement of the 5p15.2 region. Ann Rheum Dis 2013; 72:427-36. [PMID: 22956598 PMCID: PMC3691951 DOI: 10.1136/annrheumdis-2012-201742] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Accepted: 07/19/2012] [Indexed: 12/31/2022]
Abstract
BACKGROUND AND OBJECTIVES Chronic widespread pain (CWP) is a common disorder affecting ∼10% of the general population and has an estimated heritability of 48-52%. In the first large-scale genome-wide association study (GWAS) meta-analysis, we aimed to identify common genetic variants associated with CWP. METHODS We conducted a GWAS meta-analysis in 1308 female CWP cases and 5791 controls of European descent, and replicated the effects of the genetic variants with suggestive evidence for association in 1480 CWP cases and 7989 controls. Subsequently, we studied gene expression levels of the nearest genes in two chronic inflammatory pain mouse models, and examined 92 genetic variants previously described associated with pain. RESULTS The minor C-allele of rs13361160 on chromosome 5p15.2, located upstream of chaperonin-containing-TCP1-complex-5 gene (CCT5) and downstream of FAM173B, was found to be associated with a 30% higher risk of CWP (minor allele frequency=43%; OR=1.30, 95% CI 1.19 to 1.42, p=1.2×10(-8)). Combined with the replication, we observed a slightly attenuated OR of 1.17 (95% CI 1.10 to 1.24, p=4.7×10(-7)) with moderate heterogeneity (I2=28.4%). However, in a sensitivity analysis that only allowed studies with joint-specific pain, the combined association was genome-wide significant (OR=1.23, 95% CI 1.14 to 1.32, p=3.4×10(-8), I2=0%). Expression levels of Cct5 and Fam173b in mice with inflammatory pain were higher in the lumbar spinal cord, not in the lumbar dorsal root ganglions, compared to mice without pain. None of the 92 genetic variants previously described were significantly associated with pain (p>7.7×10(-4)). CONCLUSIONS We identified a common genetic variant on chromosome 5p15.2 associated with joint-specific CWP in humans. This work suggests that CCT5 and FAM173B are promising targets in the regulation of pain.
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Affiliation(s)
- Marjolein J Peters
- Department of Internal Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
- The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands
| | - Linda Broer
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Hanneke L D M Willemen
- Laboratory of Neuroimmunology and Developmental Origins of Disease, University Medical Center Utrecht, The Netherlands
| | | | - Lynne J Hocking
- Aberdeen Pain Research Collaboration (Musculoskeletal Research), University of Aberdeen, Aberdeen, UK
| | - Kate L Holliday
- Arthritis Research UK Epidemiology Unit, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Michael A Horan
- Mental Health and Neurodegeneration Group, School Community Based Medicine, University of Manchester, Manchester, UK
| | - Ingrid Meulenbelt
- Department of Medical Statistics and Bioinformatics, Section of Molecular Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tuhina Neogi
- Clinical Epidemiology Unit, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Maria Popham
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Carsten O Schmidt
- Institute for Community Medicine, University of Greifswald, Greifswald, Germany
| | - Anushka Soni
- NIHR Musculoskeletal Biomedical Research Unit, University of Oxford, Oxford, UK
| | - Ana M Valdes
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Elaine M Dennison
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Niels Eijkelkamp
- Molecular Nociception Group, University College London, London, UK
| | - Tamara B Harris
- Intramural Research Program, Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, Bethesda, Maryland, USA
| | - Deborah J Hart
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Frank J P M Huygen
- Department of Anaesthesiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Karen A Jameson
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Gareth T Jones
- Aberdeen Pain Research Collaboration (Epidemiology Group), University of Aberdeen, Aberdeen, UK
| | - Lenore J Launer
- Intramural Research Program, Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, Bethesda, Maryland, USA
| | - Hanneke J M Kerkhof
- Department of Internal Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
- The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands
| | - Marjolein de Kruijf
- Department of Internal Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
- The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands
- Department of Anaesthesiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - John McBeth
- Arthritis Research UK Epidemiology Unit, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Margreet Kloppenburg
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - William E Ollier
- Centre for Integrated Genomic Medical Research, University of Manchester, Manchester, UK
| | - Ben Oostra
- Department of Clinical Genetics, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Antony Payton
- Centre for Integrated Genomic Medical Research, University of Manchester, Manchester, UK
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Blair H Smith
- Medical Research Institute, University of Dundee, Dundee, UK
| | - Albert V Smith
- Icelandic Heart Association Research Institute, Kopavogur, Iceland
- Department of Medicine, University of Iceland, Reykjavik, Iceland
| | - Lisette Stolk
- Department of Internal Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
- The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands
| | - Alexander Teumer
- Institute of Functional Genomics, Ernst Moritz Arndt University Greifswald, University of Greifswald, Greifswald, Germany
| | - Wendy Thomson
- Arthritis Research UK Epidemiology Unit, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ke Wang
- Clinical Epidemiology Unit, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Sophie H van Wingerden
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Nigel K Arden
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
- NIHR Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK
- NIHR Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - David Felson
- Clinical Epidemiology Unit, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association Research Institute, Kopavogur, Iceland
- Department of Medicine, University of Iceland, Reykjavik, Iceland
| | - Gary J Macfarlane
- Aberdeen Pain Research Collaboration (Epidemiology Group), University of Aberdeen, Aberdeen, UK
| | - Neil Pendleton
- Mental Health and Neurodegeneration Group, School Community Based Medicine, University of Manchester, Manchester, UK
| | - P Eline Slagboom
- The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands
- Department of Medical Statistics and Bioinformatics, Section of Molecular Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Henry Völzke
- Institute for Community Medicine, University of Greifswald, Greifswald, Germany
| | - Annemieke Kavelaars
- Laboratory of Neuroimmunology and Developmental Origins of Disease, University Medical Center Utrecht, The Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Frances M K Williams
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
- The Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging (NGI-NCHA), Leiden/Rotterdam, The Netherlands
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8
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Lopes MC, Hysi PG, Verhoeven VJM, Macgregor S, Hewitt AW, Montgomery GW, Cumberland P, Vingerling JR, Young TL, van Duijn CM, Oostra B, Uitterlinden AG, Rahi JS, Mackey DA, Klaver CCW, Andrew T, Hammond CJ. Identification of a candidate gene for astigmatism. Invest Ophthalmol Vis Sci 2013; 54:1260-7. [PMID: 23322567 DOI: 10.1167/iovs.12-10463] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Astigmatism is a common refractive error that reduces vision, where the curvature and refractive power of the cornea in one meridian are less than those of the perpendicular axis. It is a complex trait likely to be influenced by both genetic and environmental factors. Twin studies of astigmatism have found approximately 60% of phenotypic variance is explained by genetic factors. This study aimed to identify susceptibility loci for astigmatism. METHODS We performed a meta-analysis of seven genome-wide association studies that included 22,100 individuals of European descent, where astigmatism was defined as the number of diopters of cylinder prescription, using fixed effect inverse variance-weighted methods. RESULTS A susceptibility locus was identified with lead single nucleotide polymorphism rs3771395 on chromosome 2p13.3 (meta-analysis, P = 1.97 × 10(-7)) in the VAX2 gene. VAX2 plays an important role in the development of the dorsoventral axis of the eye. Animal studies have shown a gradient in astigmatism along the vertical plane, with corresponding changes in refraction, particularly in the ventral field. CONCLUSIONS This finding advances the understanding of refractive error, and provides new potential pathways to be evaluated with regard to the development of astigmatism.
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Affiliation(s)
- Margarida C Lopes
- Department of Twin Research and Genetic Epidemiology, King's College London, St. Thomas' Hospital, London, United Kingdom
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9
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van Vliet R, Breedveld G, de Rijk-van Andel J, Brilstra E, Verbeek N, Verschuuren-Bemelmans C, Boon M, Samijn J, Diderich K, van de Laar I, Oostra B, Bonifati V, Maat-Kievit A. PRRT2 phenotypes and penetrance of paroxysmal kinesigenic dyskinesia and infantile convulsions. Neurology 2012; 79:777-84. [PMID: 22875091 DOI: 10.1212/wnl.0b013e3182661fe3] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To describe the phenotypes and penetrance of paroxysmal kinesigenic dyskinesia (PKD), a movement disorder characterized by attacks of involuntary movements occurring after sudden movements, infantile convulsion and choreoathetosis (ICCA) syndrome, and benign familial infantile convulsions (BFIC), caused by PRRT2 mutations. METHODS We performed clinical and genetic studies in 3 large families with ICCA, 2 smaller families with PKD, and 4 individuals with sporadic PKD. Migraine was also present in several individuals. RESULTS We detected 3 different PRRT2 heterozygous mutations: the recurrent p.Arg217Profs*8 mutation, previously reported, was identified in 2 families with ICCA, 2 families with PKD, and one individual with sporadic PKD; one novel missense mutation (p.Ser275Phe) was detected in the remaining family with ICCA; and one novel truncating mutation (p.Arg217*) was found in one individual with sporadic PKD. In the 2 remaining individuals with sporadic PKD, PRRT2 mutations were not detected. Importantly, PRRT2 mutations did not cosegregate with febrile convulsions or with migraine. The estimated penetrance of PRRT2 mutations was 61%, if only the PKD phenotype was considered; however, if infantile convulsions were also taken into account, the penetrance was nearly complete. Considering our findings and those reported in literature, 23 PRRT2 mutations explain ∼56% of the families analyzed. CONCLUSIONS PRRT2 mutations are the major cause of PKD or ICCA, but they do not seem to be involved in the etiology of febrile convulsions and migraine. The identification of PRRT2 as a major gene for the PKD-ICCA-BFIC spectrum allows better disease classification, molecular confirmation of the clinical diagnosis, and genetic testing and counseling.
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Affiliation(s)
- Rianne van Vliet
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands
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10
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Ibrahim‐Verbaas C, Demirkan A, Isaacs A, Amin N, Swieten J, Oostra B, Duijn C. P2‐035: Phosphosphingolipid levels are associated with cognitive function and level of education in healthy subjects. Alzheimers Dement 2012. [DOI: 10.1016/j.jalz.2012.05.738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - Ayse Demirkan
- Erasmus University Medical CenterRotterdamNetherlands
| | - Aaron Isaacs
- Erasmus University Medical CenterRotterdamNetherlands
| | - Najaf Amin
- Erasmus University Medical CenterRotterdamNetherlands
| | - John Swieten
- Erasmus University Medical CenterRotterdamNetherlands
| | - Ben Oostra
- Erasmus University Medical CenterRotterdamNetherlands
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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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Perry JRB, Voight BF, Yengo L, Amin N, Dupuis J, Ganser M, Grallert H, Navarro P, Li M, Qi L, Steinthorsdottir V, Scott RA, Almgren P, Arking DE, Aulchenko Y, Balkau B, Benediktsson R, Bergman RN, Boerwinkle E, Bonnycastle L, Burtt NP, Campbell H, Charpentier G, Collins FS, Gieger C, Green T, Hadjadj S, Hattersley AT, Herder C, Hofman A, Johnson AD, Kottgen A, Kraft P, Labrune Y, Langenberg C, Manning AK, Mohlke KL, Morris AP, Oostra B, Pankow J, Petersen AK, Pramstaller PP, Prokopenko I, Rathmann W, Rayner W, Roden M, Rudan I, Rybin D, Scott LJ, Sigurdsson G, Sladek R, Thorleifsson G, Thorsteinsdottir U, Tuomilehto J, Uitterlinden AG, Vivequin S, Weedon MN, Wright AF, Hu FB, Illig T, Kao L, Meigs JB, Wilson JF, Stefansson K, van Duijn C, Altschuler D, Morris AD, Boehnke M, McCarthy MI, Froguel P, Palmer CNA, Wareham NJ, Groop L, Frayling TM, Cauchi S. Stratifying type 2 diabetes cases by BMI identifies genetic risk variants in LAMA1 and enrichment for risk variants in lean compared to obese cases. PLoS Genet 2012; 8:e1002741. [PMID: 22693455 PMCID: PMC3364960 DOI: 10.1371/journal.pgen.1002741] [Citation(s) in RCA: 170] [Impact Index Per Article: 14.2] [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: 02/13/2012] [Accepted: 04/14/2012] [Indexed: 02/06/2023] Open
Abstract
Common diseases such as type 2 diabetes are phenotypically heterogeneous. Obesity is a major risk factor for type 2 diabetes, but patients vary appreciably in body mass index. We hypothesized that the genetic predisposition to the disease may be different in lean (BMI<25 Kg/m²) compared to obese cases (BMI≥30 Kg/m²). We performed two case-control genome-wide studies using two accepted cut-offs for defining individuals as overweight or obese. We used 2,112 lean type 2 diabetes cases (BMI<25 kg/m²) or 4,123 obese cases (BMI≥30 kg/m²), and 54,412 un-stratified controls. Replication was performed in 2,881 lean cases or 8,702 obese cases, and 18,957 un-stratified controls. To assess the effects of known signals, we tested the individual and combined effects of SNPs representing 36 type 2 diabetes loci. After combining data from discovery and replication datasets, we identified two signals not previously reported in Europeans. A variant (rs8090011) in the LAMA1 gene was associated with type 2 diabetes in lean cases (P = 8.4×10⁻⁹, OR = 1.13 [95% CI 1.09-1.18]), and this association was stronger than that in obese cases (P = 0.04, OR = 1.03 [95% CI 1.00-1.06]). A variant in HMG20A--previously identified in South Asians but not Europeans--was associated with type 2 diabetes in obese cases (P = 1.3×10⁻⁸, OR = 1.11 [95% CI 1.07-1.15]), although this association was not significantly stronger than that in lean cases (P = 0.02, OR = 1.09 [95% CI 1.02-1.17]). For 36 known type 2 diabetes loci, 29 had a larger odds ratio in the lean compared to obese (binomial P = 0.0002). In the lean analysis, we observed a weighted per-risk allele OR = 1.13 [95% CI 1.10-1.17], P = 3.2×10⁻¹⁴. This was larger than the same model fitted in the obese analysis where the OR = 1.06 [95% CI 1.05-1.08], P = 2.2×10⁻¹⁶. This study provides evidence that stratification of type 2 diabetes cases by BMI may help identify additional risk variants and that lean cases may have a stronger genetic predisposition to type 2 diabetes.
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Affiliation(s)
- John R. B. Perry
- Genetics of Complex Traits, Peninsula Medical School, University of Exeter, Exeter, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Benjamin F. Voight
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Loïc Yengo
- CNRS UMR 8199, Genomics of Metabolic Diseases, Lille, France
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Martha Ganser
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, Neuherberg, Germany
| | - Pau Navarro
- MRC Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Man Li
- Johns Hopkins Bloomberg School of Public Health and Epidemiology, Baltimore, Maryland, United States of America
| | - Lu Qi
- Departments of Nutrition and Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | | | - Robert A. Scott
- MRC Epidemiology Unit, Medical Research Council, Cambridge, United Kingdom
| | - Peter Almgren
- Diabetes and Endocrinology Research Unit, Department of Clinical Sciences, Lund University, Malmoe, Sweden
| | - Dan E. Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Yurii Aulchenko
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Rafn Benediktsson
- Landspitali University Hospital, Reykjavik, Iceland
- Icelandic Heart Association, Kopavogur, Iceland
| | - Richard N. Bergman
- Diabetes and Obesity Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Eric Boerwinkle
- University of Texas Health Science Center at Houston, Human Genetics Center, Houston, Texas, United States of America
| | - Lori Bonnycastle
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Noël P. Burtt
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom
| | - Guillaume Charpentier
- Corbeil-Essonnes hospital, Department of Endocrinology-Diabetology, Corbeil-Essonnes, France
| | - Francis S. Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum Muenchen, Neuherberg, Germany
| | - Todd Green
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Samy Hadjadj
- CHU Poitiers, Department of Endocrinology-Diabetology, CIC INSERM 0801, INSERM U927, University of Medical and Pharmaceutical Sciences, Poitiers, France
| | - Andrew T. Hattersley
- Genetics of Complex Traits, Peninsula Medical School, University of Exeter, Exeter, United Kingdom
| | - Christian Herder
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Andrew D. Johnson
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Anna Kottgen
- Johns Hopkins Bloomberg School of Public Health and Epidemiology, Baltimore, Maryland, United States of America
- Freiburg University Clinic, Renal Division, Freiburg, Germany
| | - Peter Kraft
- Departments of Nutrition and Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Yann Labrune
- CNRS UMR 8199, Genomics of Metabolic Diseases, Lille, France
| | - Claudia Langenberg
- MRC Epidemiology Unit, Medical Research Council, Cambridge, United Kingdom
| | - Alisa K. Manning
- Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ben Oostra
- Erasmus University Medical School, Rotterdam, The Netherlands
| | - James Pankow
- School of Public Health, Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ann-Kristin Petersen
- Institute of Genetic Epidemiology, Helmholtz Zentrum Muenchen, Neuherberg, Germany
| | - Peter P. Pramstaller
- Center for Biomedicine, 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
| | - 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
| | - Wolfgang Rathmann
- Institute of Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - William Rayner
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Michael Roden
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Metabolic Diseases, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Igor Rudan
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Denis Rybin
- Boston University Data Coordinating Center, Boston, Massachusetts, United States of America
| | - Laura J. Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Gunnar Sigurdsson
- Landspitali University Hospital, Reykjavik, Iceland
- Icelandic Heart Association, Kopavogur, Iceland
| | - Rob Sladek
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Canada
| | | | - Unnur Thorsteinsdottir
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Jaakko Tuomilehto
- Diabetes Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland
- South Ostrobothnia Central Hospital, Seinäjoki, Finland
- Red RECAVA Grupo RD06/0014/0015, Hospital Universitario La Paz, Madrid, Spain
- Centre for Vascular Prevention, Danube-University Krems, Krems, Austria
| | | | | | - Michael N. Weedon
- Genetics of Complex Traits, Peninsula Medical School, University of Exeter, Exeter, United Kingdom
| | - Alan F. Wright
- MRC Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | | | - Frank B. Hu
- Departments of Nutrition and Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Linda Kao
- Johns Hopkins Bloomberg School of Public Health and Epidemiology, Baltimore, Maryland, United States of America
| | - James B. Meigs
- General Medicine Division, Massachusetts General Hospital and Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - James F. Wilson
- Centre for Population Health Sciences, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom
| | - Kari Stefansson
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | | | - David Altschuler
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Andrew D. Morris
- Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Mark I. McCarthy
- 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
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, United Kingdom
| | - Philippe Froguel
- CNRS UMR 8199, Genomics of Metabolic Diseases, Lille, France
- Department of Genomics of Common Diseases, Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Colin N. A. Palmer
- Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, United Kingdom
| | | | - Leif Groop
- Diabetes and Endocrinology Research Unit, Department of Clinical Sciences, Lund University, Malmoe, Sweden
| | - Timothy M. Frayling
- Genetics of Complex Traits, Peninsula Medical School, University of Exeter, Exeter, United Kingdom
| | - Stéphane Cauchi
- CNRS UMR 8199, Genomics of Metabolic Diseases, Lille, France
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Scharf J, Yu D, Mathews C, Neale B, Stewart E, Fagerness J, Evans P, Gamazon E, Service S, Osiecki L, Illmann C, Cath D, King R, Dion Y, Sandor P, Barr C, Budman C, Lyon G, Grados M, Singer H, Jankovic J, Gilbert D, Hoekstra P, Heiman G, Tischfield J, State M, Robertson M, Kurlan R, Ophoff R, Gibbs JR, Cookson M, Hardy J, Singleton A, Ruiz-Linares A, Rouleau G, Heutink P, Oostra B, McMahon W, Freimer N, COX N, Pauls D. Genome-Wide Association Study of Gilles de la Tourette Syndrome (IN10-1.002). Neurology 2012. [DOI: 10.1212/wnl.78.1_meetingabstracts.in10-1.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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14
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Scharf J, Yu D, Mathews C, Neale B, Stewart E, Fagerness J, Evans P, Gamazon E, Service S, Osiecki L, Illmann C, Cath D, King R, Dion Y, Sandor P, Barr C, Budman C, Lyon G, Grados M, Singer H, Jankovic J, Gilbert D, Hoekstra P, Heiman G, Tischfield J, State M, Robertson M, Kurlan R, Ophoff R, Gibbs JR, Cookson M, Hardy J, Singleton A, Ruiz-Linares A, Rouleau G, Heutink P, Oostra B, McMahon W, Freimer N, COX N, Pauls D. Genome-Wide Association Study of Gilles de la Tourette Syndrome (S32.006). Neurology 2012. [DOI: 10.1212/wnl.78.1_meetingabstracts.s32.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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15
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Heid IM, Jackson AU, Randall JC, Winkler TW, Qi L, Steinthorsdottir V, Thorleifsson G, Zillikens MC, Speliotes EK, Mägi R, Workalemahu T, White CC, Bouatia-Naji N, Harris TB, Berndt SI, Ingelsson E, Willer CJ, Weedon MN, Luan J, Vedantam S, Esko T, Kilpeläinen TO, Kutalik Z, Li S, Monda KL, Dixon AL, Holmes CC, Kaplan LM, Liang L, Min JL, Moffatt MF, Molony C, Nicholson G, Schadt EE, Zondervan KT, Feitosa MF, Ferreira T, Allen HL, Weyant RJ, Wheeler E, Wood AR, Estrada K, Goddard ME, Lettre G, Mangino M, Nyholt DR, Purcell S, Vernon Smith A, Visscher PM, Yang J, McCarroll SA, Nemesh J, Voight BF, Absher D, Amin N, Aspelund T, Coin L, Glazer NL, Hayward C, Heard-Costa NL, Hottenga JJ, Johansson Å, Johnson T, Kaakinen M, Kapur K, Ketkar S, Knowles JW, Kraft P, Kraja AT, Lamina C, Leitzmann MF, McKnight B, Morris AP, Ong KK, Perry JRB, Peters MJ, Polasek O, Prokopenko I, Rayner NW, Ripatti S, Rivadeneira F, Robertson NR, Sanna S, Sovio U, Surakka I, Teumer A, van Wingerden S, Vitart V, Zhao JH, Cavalcanti-Proença C, Chines PS, Fisher E, Kulzer JR, Lecoeur C, Narisu N, Sandholt C, Scott LJ, Silander K, Stark K, Tammesoo ML, Teslovich TM, Timpson NJ, Watanabe RM, Welch R, Chasman DI, Cooper MN, Jansson JO, Kettunen J, Lawrence RW, Pellikka N, Perola M, Vandenput L, Alavere H, Almgren P, Atwood LD, Bennett AJ, Biffar R, Bonnycastle LL, Bornstein SR, Buchanan TA, Campbell H, Day INM, Dei M, Dörr M, Elliott P, Erdos MR, Eriksson JG, Freimer NB, Fu M, Gaget S, Geus EJC, Gjesing AP, Grallert H, Gräßler J, Groves CJ, Guiducci C, Hartikainen AL, Hassanali N, Havulinna AS, Herzig KH, Hicks AA, Hui J, Igl W, Jousilahti P, Jula A, Kajantie E, Kinnunen L, Kolcic I, Koskinen S, Kovacs P, Kroemer HK, Krzelj V, Kuusisto J, Kvaloy K, Laitinen J, Lantieri O, Lathrop GM, Lokki ML, Luben RN, Ludwig B, McArdle WL, McCarthy A, Morken MA, Nelis M, Neville MJ, Paré G, Parker AN, Peden JF, Pichler I, Pietiläinen KH, Platou CGP, Pouta A, Ridderstråle M, Samani NJ, Saramies J, Sinisalo J, Smit JH, Strawbridge RJ, Stringham HM, Swift AJ, Teder-Laving M, Thomson B, Usala G, van Meurs JBJ, van Ommen GJ, Vatin V, Volpato CB, Wallaschofski H, Walters GB, Widen E, Wild SH, Willemsen G, Witte DR, Zgaga L, Zitting P, Beilby JP, James AL, Kähönen M, Lehtimäki T, Nieminen MS, Ohlsson C, Palmer LJ, Raitakari O, Ridker PM, Stumvoll M, Tönjes A, Viikari J, Balkau B, Ben-Shlomo Y, Bergman RN, Boeing H, Smith GD, Ebrahim S, Froguel P, Hansen T, Hengstenberg C, Hveem K, Isomaa B, Jørgensen T, Karpe F, Khaw KT, Laakso M, Lawlor DA, Marre M, Meitinger T, Metspalu A, Midthjell K, Pedersen O, Salomaa V, Schwarz PEH, Tuomi T, Tuomilehto J, Valle TT, Wareham NJ, Arnold AM, Beckmann JS, Bergmann S, Boerwinkle E, Boomsma DI, Caulfield MJ, Collins FS, Eiriksdottir G, Gudnason V, Gyllensten U, Hamsten A, Hattersley AT, Hofman A, Hu FB, Illig T, Iribarren C, Jarvelin MR, Kao WHL, Kaprio J, Launer LJ, Munroe PB, Oostra B, Penninx BW, Pramstaller PP, Psaty BM, Quertermous T, Rissanen A, Rudan I, Shuldiner AR, Soranzo N, Spector TD, Syvanen AC, Uda M, Uitterlinden A, Völzke H, Vollenweider P, Wilson JF, Witteman JC, Wright AF, Abecasis GR, Boehnke M, Borecki IB, Deloukas P, Frayling TM, Groop LC, Haritunians T, Hunter DJ, Kaplan RC, North KE, O'Connell JR, Peltonen L, Schlessinger D, Strachan DP, Hirschhorn JN, Assimes TL, Wichmann HE, Thorsteinsdottir U, van Duijn CM, Stefansson K, Cupples LA, Loos RJF, Barroso I, McCarthy MI, Fox CS, Mohlke KL, Lindgren CM. Erratum: Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Nat Genet 2011. [DOI: 10.1038/ng1111-1164a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Bis JC, Kavousi M, Franceschini N, Isaacs A, Abecasis GR, Schminke U, Post WS, Smith AV, Cupples LA, Markus HS, Schmidt R, Huffman JE, Lehtimäki T, Baumert J, Münzel T, Heckbert SR, Dehghan A, North K, Oostra B, Bevan S, Stoegerer EM, Hayward C, Raitakari O, Meisinger C, Schillert A, Sanna S, Völzke H, Cheng YC, Thorsson B, Fox CS, Rice K, Rivadeneira F, Nambi V, Halperin E, Petrovic KE, Peltonen L, Wichmann HE, Schnabel RB, Dörr M, Parsa A, Aspelund T, Demissie S, Kathiresan S, Reilly MP, Taylor K, Uitterlinden A, Couper DJ, Sitzer M, Kähönen M, Illig T, Wild PS, Orru M, Lüdemann J, Shuldiner AR, Eiriksdottir G, White CC, Rotter JI, Hofman A, Seissler J, Zeller T, Usala G, Ernst F, Launer LJ, D'Agostino RB, O'Leary DH, Ballantyne C, Thiery J, Ziegler A, Lakatta EG, Chilukoti RK, Harris TB, Wolf PA, Psaty BM, Polak JF, Li X, Rathmann W, Uda M, Boerwinkle E, Klopp N, Schmidt H, Wilson JF, Viikari J, Koenig W, Blankenberg S, Newman AB, Witteman J, Heiss G, Duijn CV, Scuteri A, Homuth G, Mitchell BD, Gudnason V, O'Donnell CJ. Meta-analysis of genome-wide association studies from the CHARGE consortium identifies common variants associated with carotid intima media thickness and plaque. Nat Genet 2011; 43:940-7. [PMID: 21909108 PMCID: PMC3257519 DOI: 10.1038/ng.920] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 08/02/2011] [Indexed: 01/17/2023]
Affiliation(s)
- Joshua C Bis
- Cardiovascular Health Research Unit and Department of Medicine, University of Washington, Seattle, Washington, USA.
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17
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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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Collins SC, Coffee B, Benke PJ, Berry-Kravis E, Gilbert F, Oostra B, Halley D, Zwick ME, Cutler DJ, Warren ST. Array-based FMR1 sequencing and deletion analysis in patients with a fragile X syndrome-like phenotype. PLoS One 2010; 5:e9476. [PMID: 20221430 PMCID: PMC2832695 DOI: 10.1371/journal.pone.0009476] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 02/11/2010] [Indexed: 11/18/2022] Open
Abstract
Background Fragile X syndrome (FXS) is caused by loss of function mutations in the FMR1 gene. Trinucleotide CGG-repeat expansions, resulting in FMR1 gene silencing, are the most common mutations observed at this locus. Even though the repeat expansion mutation is a functional null mutation, few conventional mutations have been identified at this locus, largely due to the clinical laboratory focus on the repeat tract. Methodology/Principal Findings To more thoroughly evaluate the frequency of conventional mutations in FXS-like patients, we used an array-based method to sequence FMR1 in 51 unrelated males exhibiting several features characteristic of FXS but with normal CGG-repeat tracts of FMR1. One patient was identified with a deletion in FMR1, but none of the patients were found to have other conventional mutations. Conclusions/Significance These data suggest that missense mutations in FMR1 are not a common cause of the FXS phenotype in patients who have normal-length CGG-repeat tracts. However, screening for small deletions of FMR1 may be of clinically utility.
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Affiliation(s)
- Stephen C. Collins
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Brad Coffee
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Paul J. Benke
- Joe DiMaggio Children's Hospital, Hollywood, Florida, United States of America
| | - Elizabeth Berry-Kravis
- Departments of Pediatrics and Neurological Sciences, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Fred Gilbert
- Department of Pediatrics, Weill Cornell Medical College, New York, New York, United States of America
| | - Ben Oostra
- Department of Clinical Genetics, Erasmus University, Rotterdam, The Netherlands
| | - Dicky Halley
- Department of Clinical Genetics, Erasmus University, Rotterdam, The Netherlands
| | - Michael E. Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - David J. Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Stephen T. Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Departments of Pediatrics and Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail:
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Rivadeneira F, Styrkársdottir U, Estrada K, Halldórsson BV, Hsu YH, Richards JB, Zillikens MC, Kavvoura FK, Amin N, Aulchenko YS, Cupples LA, Deloukas P, Demissie S, Grundberg E, Hofman A, Kong A, Karasik D, van Meurs JB, Oostra B, Pastinen T, Pols HAP, Sigurdsson G, Soranzo N, Thorleifsson G, Thorsteinsdottir U, Williams FMK, Wilson SG, Zhou Y, Ralston SH, van Duijn CM, Spector T, Kiel DP, Stefansson K, Ioannidis JPA, Uitterlinden AG. Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies. Nat Genet 2009; 41:1199-206. [PMID: 19801982 PMCID: PMC2783489 DOI: 10.1038/ng.446] [Citation(s) in RCA: 585] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Accepted: 07/21/2009] [Indexed: 12/15/2022]
Abstract
Bone mineral density (BMD) is a heritable complex trait used in the clinical diagnosis of osteoporosis and the assessment of fracture risk. We performed meta-analysis of five genome-wide association studies of femoral neck and lumbar spine BMD in 19,195 subjects of Northern European descent. We identified 20 BMD loci that reached genome-wide significance (GWS; P < 5 x 10(-8)), of which 13 map to regions not previously associated with this trait: 1p31.3 (GPR177), 2p21 (SPTBN1), 3p22 (CTNNB1), 4q21.1 (MEPE), 5q14 (MEF2C), 7p14 (STARD3NL), 7q21.3 (FLJ42280), 11p11.2 (LRP4, ARHGAP1, F2), 11p14.1 (DCDC5), 11p15 (SOX6), 16q24 (FOXL1), 17q21 (HDAC5) and 17q12 (CRHR1). The meta-analysis also confirmed at GWS level seven known BMD loci on 1p36 (ZBTB40), 6q25 (ESR1), 8q24 (TNFRSF11B), 11q13.4 (LRP5), 12q13 (SP7), 13q14 (TNFSF11) and 18q21 (TNFRSF11A). The many SNPs associated with BMD map to genes in signaling pathways with relevance to bone metabolism and highlight the complex genetic architecture that underlies osteoporosis and variation in BMD.
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20
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Infante J, Berciano J, Sánchez-Juan P, García A, Di Fonzo A, Breedveld G, Oostra B, Bonifati V. Pseudo-orthostatic and resting leg tremor in a large Spanish family with homozygous truncating parkin mutation. Mov Disord 2009; 24:144-7. [PMID: 18951541 DOI: 10.1002/mds.22349] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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21
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Bonifati V, Wu-Chou YH, Schweiger D, Fonzo AD, Lu CS, Oostra B, Nichols W.C, Elsaesser V.E, Pankratz N., Pauciulo M.W, Marek D.K, Halter C.A, Rudolph A., Foroud T.. LRRK2 MUTATION ANALYSIS IN PARKINSON DISEASE FAMILIES WITH EVIDENCE OF LINKAGE TO PARK8. Neurology 2008; 70:2348; author reply 2348-9. [DOI: 10.1212/01.wnl.0000317005.06662.01] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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22
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Arias-Vásquez A, de Lau L, Pardo L, Liu F, Feng BJ, Bertoli-Avella A, Isaacs A, Aulchenko Y, Hofman A, Oostra B, Breteler M, van Duijn C. Relationship of the Ubiquilin 1 gene with Alzheimer's and Parkinson's disease and cognitive function. Neurosci Lett 2007; 424:1-5. [PMID: 17709205 DOI: 10.1016/j.neulet.2007.07.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 07/06/2007] [Accepted: 07/06/2007] [Indexed: 12/18/2022]
Abstract
Ubiquilin 1 (UBQLN1) is involved in the ubiquitination machinery, which has been implicated in Alzheimer's disease (AD) as well as Parkinson's disease (PD). A polymorphism in the gene encoding for UBQLN1 has been previously associated with a higher risk of AD. We studied the role of the SNP rs12344615 on the UBQLN 1 gene in AD, PD and cognitive function in a population-based study, the Rotterdam Study, and a family-based study embedded in the genetic research in isolated population (GRIP) program. The Rotterdam Study includes 549 patients with AD and 157 patients with PD. The GRIP program includes a series of 123 patients with AD and a study of 1049 persons who are characterized for cognitive function. Data were analysed using logistic and multiple regression analysis. We found no significant difference in risk of AD or PD by the UBQLN1 SNP rs12344615 in our overall and stratified analyses in the Rotterdam Study. In our family-based study, we did not find evidence for linkage of AD to the region including the UBQLN1 gene. In the family-based study we also failed to detect an effect of this polymorphism on cognitive function. Our results suggest that it is unlikely that the SNP rs12344615 of the UBQLN1 gene is related to the onset of AD, PD or cognitive function.
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Cossu G, Modugno N, Deriu M, Murgia D, Serra G, Melis M, Breddveld G, Simons E, Oostra B, Bonifati V. 2.117 Clinical spectrum of a large Sardinian family with Parkinson's disease. Parkinsonism Relat Disord 2007. [DOI: 10.1016/s1353-8020(08)70609-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Arias A, Isaacs A, Aulchenko Y, Hofman A, Breteler M, Oostra B, Duijn C. P1–309: Evidence for interaction between the Cholesteryl ester transfer protein (CETP) gene and APOE in late onset Alzheimer's disease. Alzheimers Dement 2006. [DOI: 10.1016/j.jalz.2006.05.687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Alejandro Arias
- Department of Epidemiology & BiostatisticsErasmus Medical CentreRotterdamThe Netherlands
| | - Aaron Isaacs
- Department of Epidemiology & BiostatisticsErasmus Medical CentreRotterdamThe Netherlands
| | - Yurii Aulchenko
- Department of Epidemiology & BiostatisticsErasmus Medical CentreRotterdamThe Netherlands
| | - Albert Hofman
- Department of Epidemiology & BiostatisticsErasmus Medical CentreRotterdamThe Netherlands
| | - Monique Breteler
- Department of Epidemiology & BiostatisticsErasmus Medical CentreRotterdamThe Netherlands
| | - Ben Oostra
- Department of Clinical GeneticsErasmus Medical CentreRotterdamThe Netherlands
| | - Cornelia Duijn
- Department of Epidemiology & BiostatisticsErasmus Medical CentreRotterdamThe Netherlands
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Service S, DeYoung J, Karayiorgou M, Roos JL, Pretorious H, Bedoya G, Ospina J, Ruiz-Linares A, Macedo A, Palha JA, Heutink P, Aulchenko Y, Oostra B, van Duijn C, Jarvelin MR, Varilo T, Peddle L, Rahman P, Piras G, Monne M, Murray S, Galver L, Peltonen L, Sabatti C, Collins A, Freimer N. Magnitude and distribution of linkage disequilibrium in population isolates and implications for genome-wide association studies. Nat Genet 2006; 38:556-60. [PMID: 16582909 DOI: 10.1038/ng1770] [Citation(s) in RCA: 183] [Impact Index Per Article: 10.2] [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: 11/08/2005] [Accepted: 02/28/2006] [Indexed: 11/09/2022]
Abstract
The genome-wide distribution of linkage disequilibrium (LD) determines the strategy for selecting markers for association studies, but it varies between populations. We assayed LD in large samples (200 individuals) from each of 11 well-described population isolates and an outbred European-derived sample, using SNP markers spaced across chromosome 22. Most isolates show substantially higher levels of LD than the outbred sample and many fewer regions of very low LD (termed 'holes'). Young isolates known to have had relatively few founders show particularly extensive LD with very few holes; these populations offer substantial advantages for genome-wide association mapping.
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Affiliation(s)
- Susan Service
- Center for Neurobehavioral Genetics, University of California, Los Angeles, California 90095, USA
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26
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Sharma M, Mueller JC, Zimprich A, Lichtner P, Hofer A, Leitner P, Maass S, Berg D, Dürr A, Bonifati V, De Michele G, Oostra B, Brice A, Wood NW, Muller-Myhsok B, Gasser T. The sepiapterin reductase gene region reveals association in the PARK3 locus: analysis of familial and sporadic Parkinson's disease in European populations. J Med Genet 2006; 43:557-62. [PMID: 16443856 PMCID: PMC2593029 DOI: 10.1136/jmg.2005.039149] [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] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Parkinson's disease is a genetically complex disease with mixed mode of inheritance. Recently, a haplotype across the sepiapterin reductase (SPR) gene, which is located in the PARK3 linkage region, was shown to modulate age of onset of Parkinson's disease in sibships from North America. OBJECTIVE To make a thorough assessment of the SPR gene region in sporadic Parkinson's disease. METHODS A linkage study in 122 European sibship families with five microsatellite and 17 single nucleotide polymorphism (SNP) markers in and around the SPR gene region, and an association analysis in 340 sporadic cases of Parkinson's disease and 680 control subjects from Germany with 40 SNPs. Linkage was evaluated by non-parametric linkage scores and genotypic or haplotype association was tested by regression analysis, assuming different risk effect models. RESULTS Significant LOD scores between 2 and 3 were obtained at the two SPR-flanking markers D2S2110 and D2S1394 and seven SNP markers around the SPR gene. We found the previously reported promoter SNP rs1876487 also significantly associated with age of onset in our sib pair families (p-value 0.02). One strong linkage disequilibrium (LD) block of 45 kb including the entire SPR gene was observed. Within this LD block all 14 inter-correlated SNPs were significantly associated with Parkinson's disease affection status (p-value 0.004). CONCLUSIONS DNA polymorphisms in a highly intercorrelated LD block, which includes the SPR gene, appear to be associated with both sporadic and familial Parkinson's disease. This confirms a previous study showing that SPR potentially modulates the onset of or risk for Parkinson's disease.
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Affiliation(s)
- M Sharma
- Hertie-Institute for Clinical Brain Research, Department for Neurodegenerative Diseases, University of Tübingen, Hoppe-Seyler Str 3, 72076 Tübingen, Germany
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Martinez M, Brice A, Vaughan JR, Zimprich A, Breteler MMB, Meco G, Filla A, Farrer MJ, Bétard C, Hardy J, De Michele G, Bonifati V, Oostra B, Gasser T, Wood NW, Dürr A. Genome-wide scan linkage analysis for Parkinson's disease: the European genetic study of Parkinson's disease. J Med Genet 2005; 41:900-7. [PMID: 15591275 PMCID: PMC1735631 DOI: 10.1136/jmg.2004.022632] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVE To undertake a full genome-wide screen for Parkinson's disease susceptibility loci. METHODS A genome-wide linkage study was undertaken in 227 affected sibling pairs from 199 pedigrees with Parkinson's disease. The pedigree sample consisted of 188 pedigrees from five European countries, and 11 from the USA. Individuals were genotyped for 391 microsatellite markers at approximately 10 cM intervals throughout the genome. Multipoint model-free affected sibling pair linkage analyses were carried out using the MLS (maximum LOD score) test. RESULTS There were six chromosomal regions with maximum MLS peaks of 1 or greater (pointwise p<0.018). Four of these chromosomal regions appear to be newly identified regions, and the highest MLS values were obtained on chromosomes 11q (MLS = 1.60, at 91 cM, D11S4175) and 7p (MLS = 1.51, at 5 cM, D7S531). The remaining two MLS peaks, on 2p11-q12 and 5q23, are consistent with excess sharing in regions reported by other studies. The highest MLS peak was observed on chromosome 2p11-q12 (MLS = 2.04, between markers D2S2216 and D2S160), within a relatively short distance (approximately 17 cM) from the PARK3 region. Although a stronger support of linkage to this region was observed in the late age of onset subgroup of families, these differences were not significant. The peak on 5q23 (MLS = 1.05, at 130 cM, D5S471) coincides with the region identified by three other genome scans. All peak locations fell within a 10 cM distance. CONCLUSIONS These stratified linkage analyses suggest linkage heterogeneity within the sample across the 2p11-q12 and 5q23 regions, with these two regions contributing independently to Parkinson's disease susceptibility.
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Affiliation(s)
- M Martinez
- Unité de Recherche INSERM EMI00-06, Tour Evry 2, 523 Place des Terrasses de l'Agora, Evry cedex 91068, France.
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Breedveld G, de Coo IF, Lequin MH, Arts WFM, Heutink P, Gould DB, John SWM, Oostra B, Mancini GMS. Novel mutations in three families confirm a major role of COL4A1 in hereditary porencephaly. J Med Genet 2005; 43:490-5. [PMID: 16107487 PMCID: PMC2593028 DOI: 10.1136/jmg.2005.035584] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Porencephaly (cystic cavities of the brain) is caused by perinatal vascular accidents from various causes. Several familial cases have been described and autosomal dominant inheritance linked to chromosome 13q has been suggested. COL4A1 is an essential component in basal membrane stability. Mouse mutants bearing an in-frame deletion of exon 40 of Col4a1 either die from haemorrhage in the perinatal period or have porencephaly in survivors. A report of inherited mutations in COL4A1 in two families has shown that familial porencephaly may have the same cause in humans. OBJECTIVE To describe three novel COL4A1 mutations. RESULTS The three mutations occurred in three unrelated Dutch families. There were two missense mutations of glycine residues predicted to result in abnormal collagen IV assembly, and one mutation predicted to abolish the traditional COL4A1 start codon. The last mutation was also present in an asymptomatic obligate carrier with white matter abnormalities on brain magnetic resonance imaging. CONCLUSIONS This observation confirms COL4A1 as a major locus for genetic predisposition to perinatal cerebral haemorrhage and porencephaly and suggests variable expression of COL4A1 mutations.
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Affiliation(s)
- G Breedveld
- Department of Clinical Genetics, Erasmus University Medical Centre, PO Box 1738, 3000 DR Rotterdam, Netherlands
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Abstract
The genetic make-up of genetically isolated populations may differ from a general population as a result of genetic drift and founder effects. We assessed the extent of this deviation in a recently isolated population located in the southwest of the Netherlands and studied as part of the Genetic Research in Isolated Population (GRIP) program. A gene-dropping experiment was performed in a large pedigree from this isolate, assuming different initial frequencies in the population founders came from. Allelic frequencies in the last generations of this pedigree were estimated. Simulation analysis showed large fluctuations, as measured by variation coefficient and sufficient loss probability, when initial frequencies were lower than or equal to 1%. For initial frequencies larger than 1% the fluctuations were small. We also analyzed mean heterozygosity and allele diversity of 592 markers in a random sample from the GRIP population. The results were compared with a general population (CEPH sample), old large isolate (Icelandic sample) and the small-sized population of Talana (Sardinia). GRIP mean heterozygosity and mean number of alleles were significantly lower as compared with CEPH and Iceland, but much higher when compared with the Talana population. We also concluded that the findings from the GRIP population for common variants (>1%) are likely to be extendable to other young isolates in Europe as well as to outbred populations.
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Affiliation(s)
- L M Pardo
- Genetic Epidemiology Unit, Department of Epidemiology & Biostatistics, Erasmus Medical Center Rotterdam, The Netherlands
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31
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Pietrobono R, Tabolacci E, Zalfa F, Zito I, Terracciano A, Moscato U, Bagni C, Oostra B, Chiurazzi P, Neri G. Molecular dissection of the events leading to inactivation of the FMR1 gene. Hum Mol Genet 2004; 14:267-77. [PMID: 15563507 DOI: 10.1093/hmg/ddi024] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [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] [Indexed: 12/22/2022] Open
Abstract
The analysis of a lymphoblastoid cell line (5106), derived from a rare individual of normal intelligence with an unmethylated full mutation of the FMR1 gene, allowed us to reconstruct the chain of molecular events leading to the FMR1 inactivation and to fragile X syndrome. We found that lack of DNA methylation of the entire promoter region, including the expanded CGG repeat, correlates with methylation of lysine 4 residue on the N-tail of histone H3 (H3-K4), as in normal controls. Normal levels of FMR1 mRNA were detected by real-time fluorescent RT-PCR (0.8-1.4 times compared with a control sample), but mRNA translation was less efficient (-40%), as judged by polysome profiling, resulting in reduced levels of FMRP protein (approximately 30% of a normal control). These results underline once more that CGG repeat amplification per se does not prevent FMR1 transcription and FMRP production in the absence of DNA methylation. Surprisingly, we found by chromatin immunoprecipitation that cell line 5106 has deacetylated histones H3 and H4 as well as methylated lysine 9 on histone H3 (H3-K9), like fragile X cell lines, in both the promoter and exon 1. This indicates that these two epigenetic marks (i.e. histone deacetylation and H3-K9 methylation) can be established in the absence of DNA methylation and do not interfere with active gene transcription, contrary to expectation. Our results also suggest that the molecular pathways regulating DNA and H3-K4 methylation are independent from those regulating histone acetylation and H3-K9 methylation.
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Aulchenko YS, Heutink P, Mackay I, Bertoli-Avella AM, Pullen J, Vaessen N, Rademaker TAM, Sandkuijl LA, Cardon L, Oostra B, van Duijn CM. Linkage disequilibrium in young genetically isolated Dutch population. Eur J Hum Genet 2004; 12:527-34. [PMID: 15054401 DOI: 10.1038/sj.ejhg.5201188] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The design and feasibility of genetic studies of complex diseases are critically dependent on the extent and distribution of linkage disequilibrium (LD) across the genome and between different populations. We have examined genomewide and region-specific LD in a young genetically isolated population identified in the Netherlands by genotyping approximately 800 Short Tandem Repeat markers distributed genomewide across 58 individuals. Several regions were analyzed further using a denser marker map. The permutation-corrected measure of LD was used for analysis. A significant (P<0.0004) relation between LD and genetic distance on a genomewide scale was found. Distance explained 4% of the total LD variation. For fine-mapping data, distance accounted for a larger proportion of LD variation (up to 39%). A notable similarity in the genomewide distribution of LD was revealed between this population and other young genetically isolated populations from Micronesia and Costa Rica. Our study population and experiment was simulated in silico to confirm our knowledge of the history of the population. High agreement was observed between results of analysis of simulated and empirical data. We conclude that our population shows a high level of LD similar to that demonstrated previously in other young genetic isolates. In Europe, there may be a large number of young genetically isolated populations that are similar in history to ours. In these populations, a similar degree of LD is expected and thus they may be effectively used for linkage or LD mapping.
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Affiliation(s)
- Yurii S Aulchenko
- Department of Epidemiology and Biostatistics, Erasmus Medical Center Rotterdam, The Netherlands.
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Bonifati V, Rizzu P, Squitieri F, Krieger E, Vanacore N, van Swieten JC, Brice A, van Duijn CM, Oostra B, Meco G, Heutink P. DJ-1( PARK7), a novel gene for autosomal recessive, early onset parkinsonism. Neurol Sci 2004; 24:159-60. [PMID: 14598065 DOI: 10.1007/s10072-003-0108-0] [Citation(s) in RCA: 286] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Four chromosomal loci ( PARK2, PARK6, PARK7, and PARK9) associated with autosomal recessive, early onset parkinsonism are known. We mapped the PARK7 locus to chromosome 1p36 in a large family from a genetically isolated population in the Netherlands, and confirmed this linkage in an Italian family. By positional cloning within the refined PARK7 critical region we recently identified mutations in the DJ-1 gene in the two PARK7-linked families. The function of DJ-1 remains largely unknown, but evidence from genetic studies on the yeast DJ-1 homologue, and biochemical studies in murine and human cell lines, suggests a role for DJ-1 as an antioxidant and/or a molecular chaperone. Elucidating the role of DJ-1 will lead to a better understanding of the pathogenesis of DJ-1-related and common forms of Parkinson's disease.
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Affiliation(s)
- V Bonifati
- Department of Clinical Genetics, Erasmus Medical Center Rotterdam, 1738 DR Rotterdam, The Netherlands
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Aziz M, Stathopulu E, Callias M, Taylor C, Turk J, Oostra B, Willemsen R, Patton M. Clinical features of boys with fragile X premutations and intermediate alleles. Am J Med Genet B Neuropsychiatr Genet 2003; 121B:119-27. [PMID: 12898586 DOI: 10.1002/ajmg.b.20030] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.3] [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] [Indexed: 11/09/2022]
Abstract
Fragile X syndrome has a characteristic behavioural and physical phenotype. Clinical experience and case reports suggest that boys with premutations and intermediate alleles may have similar, but possibly milder, clinical features than those with the full mutation. We conducted detailed physical, psychiatric, psychological and speech and language evaluations on a clinical series of 10 boys, with either premutation or intermediate CGG triplet expansions. Wherever possible we measured the levels of FMR1 protein in participants' hair roots. Many participants demonstrated striking resemblance in their clinical picture, behavioural and physical, to individuals with the fragile X syndrome full mutation. However, protein expression was normal in all participants where it was assessed, despite large variation in CGG triplet repeats. We propose that the findings are unlikely to be attributable to ascertainment bias alone. Replication on larger independent samples is required to confirm our impression that fragile X premutations and intermediate alleles may be associated with important developmental disabilities and physical features.
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Affiliation(s)
- Monica Aziz
- Child Mental Health Learning Disability Service, South-West London & St. George's Mental Health NHS Trust, United Kingdom.
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35
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Dekker M, Bonifati V, van Swieten J, Leenders N, Galjaard RJ, Snijders P, Horstink M, Heutink P, Oostra B, van Duijn C. Clinical features and neuroimaging of PARK7-linked parkinsonism. Mov Disord 2003; 18:751-7. [PMID: 12815653 DOI: 10.1002/mds.10422] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We recently reported linkage to chromosome 1p36 (the PARK7-locus) in a family with early-onset parkinsonism. Linkage to this locus has since been confirmed in an independent data set. We describe clinical and neuroimaging features of the 4 patients in the original PARK7-linked kindred. Age at onset of parkinsonism varied from 27 to 40 years. Clinical progression was slow, and response to dopaminergic therapy good. The clinical spectrum ranged from mild hypokinesia and rigidity, to severe parkinsonism with levodopa-induced dyskinesias and motor fluctuation. Three of four patients with PARK7-linked parkinsonism exhibited psychiatric disturbances. Structural neuroimaging was unremarkable, but functional imaging of the brain, carried out in 3 patients, showed significant evidence for a presynaptic dopamine deficit, and assessment of cerebral glucose metabolism, as carried out in 1 patient, showed possible cerebellar involvement.
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Affiliation(s)
- Marieke Dekker
- Genetic-Epidemiologic Unit, Departments of Epidemiology and Biostatistics and Clinical Genetics, Erasmus Medical Centre Rotterdam, The Netherlands.
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Willemsen R, Smits A, Severijnen LA, Jansen M, Jacobs A, De Bruyn E, Oostra B. Predictive testing for cognitive functioning in female carriers of the fragile X syndrome using hair root analysis. J Med Genet 2003; 40:377-9. [PMID: 12746404 PMCID: PMC1735463 DOI: 10.1136/jmg.40.5.377] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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37
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Zalfa F, Giorgi M, Primerano B, Moro A, Di Penta A, Reis S, Oostra B, Bagni C. The fragile X syndrome protein FMRP associates with BC1 RNA and regulates the translation of specific mRNAs at synapses. Cell 2003; 112:317-27. [PMID: 12581522 DOI: 10.1016/s0092-8674(03)00079-5] [Citation(s) in RCA: 519] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The Fragile X syndrome, which results from the absence of functional FMRP protein, is the most common heritable form of mental retardation. Here, we show that FMRP acts as a translational repressor of specific mRNAs at synapses. Interestingly, FMRP associates not only with these target mRNAs, but also with the dendritic, non-translatable RNA BC1. Blocking of BC1 inhibits the interaction of FMRP with its target mRNAs. Furthermore, BC1 binds directly to FMRP and can also associate, in the absence of any protein, with the mRNAs regulated by FMRP. This suggests a mechanism where BC1 could determine the specificity of FMRP function by linking the regulated mRNAs and FMRP. Thus, when FMRP is not present, loss of translational repression of specific mRNAs at synapses could result in synaptic dysfunction phenotype of Fragile X patients.
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Affiliation(s)
- Francesca Zalfa
- Dipartimento di Biologia, Università di Roma, Tor Vergata, Via della Ricerca Scientifica, 00133 Roma, Italy
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38
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De Diego Otero Y, Severijnen LA, van Cappellen G, Schrier M, Oostra B, Willemsen R. Transport of fragile X mental retardation protein via granules in neurites of PC12 cells. Mol Cell Biol 2002; 22:8332-41. [PMID: 12417734 PMCID: PMC134063 DOI: 10.1128/mcb.22.23.8332-8341.2002] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.2] [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] [Indexed: 11/20/2022] Open
Abstract
Lack of fragile X mental retardation protein (FMRP) causes fragile X syndrome, a common form of inherited mental retardation. FMRP is an RNA binding protein thought to be involved in translation efficiency and/or trafficking of certain mRNAs. Recently, a subset of mRNAs to which FMRP binds with high affinity has been identified. These FMRP-associated mRNAs contain an intramolecular G-quartet structure. In neurons, dendritic mRNAs are involved in local synthesis of proteins in response to synaptic activity, and this represents a mechanism for synaptic plasticity. To determine the role of FMRP in dendritic mRNA transport, we have generated a stably FMR1-enhanced green fluorescent protein (EGFP)-transfected PC12 cell line with an inducible expression system (Tet-On) for regulated expression of the FMRP-GFP fusion protein. After doxycycline induction, FMRP-GFP was localized in granules in the neurites of PC12 cells. By using time-lapse microscopy, the trafficking of FMRP-GFP granules into the neurites of living PC12 cells was demonstrated. Motile FMRP-GFP granules displayed two types of movements: oscillatory (bidirectional) and unidirectional anterograde. The average velocity of the granules was 0.19 micro m/s with a maximum speed of 0.71 micro m/s. In addition, we showed that the movement of FMRP-GFP labeled granules into the neurites was microtubule dependent. Colocalization studies further showed that the FMRP-GFP labeled granules also contained RNA, ribosomal subunits, kinesin heavy chain, and FXR1P molecules. This report is the first example of trafficking of RNA-containing granules with FMRP as a core constituent in living PC12 cells.
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Affiliation(s)
- Yolanda De Diego Otero
- CBG Department of Clinical Genetics. Department of Endocrinology and Reproduction, Erasmus University, Rotterdam, The Netherlands
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39
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Bonifati V, Dekker MCJ, Vanacore N, Fabbrini G, Squitieri F, Marconi R, Antonini A, Brustenghi P, Dalla Libera A, De Mari M, Stocchi F, Montagna P, Gallai V, Rizzu P, van Swieten JC, Oostra B, van Duijn CM, Meco G, Heutink P. Autosomal recessive early onset parkinsonism is linked to three loci: PARK2, PARK6, and PARK7. Neurol Sci 2002; 23 Suppl 2:S59-60. [PMID: 12548343 DOI: 10.1007/s100720200069] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Autosomal recessive, early onset parkinsonism (AREP) is genetically heterogeneous. Mutations in the parkin gene (PARK2 locus, chromosome 6q) account for up to 50% of AREP families. The parkin protein displays ubiquitin-ligase activity for different targets, which accumulate in the brain of patients with parkin defect and might cause neurodegeneration. Two new AREP loci (PARK6 and PARK7) have been recently mapped on chromosome 1p and confirmed in independent datasets, suggesting that both might be frequent. The three AREP forms display similar clinical phenotypes. Recruiting new families will help cloning the defective genes at PARK6 and PARK7 loci. This will contribute to unraveling the pathogenesis of AREP, and it is also expected to foster our understanding of molecular events underlying classic Parkinson's disease.
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Affiliation(s)
- V Bonifati
- Department of Neurological Sciences, La Sapienza University, Viale dell'Università 30, I-00185 Rome, Italy
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40
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Pietrobono R, Pomponi MG, Tabolacci E, Oostra B, Chiurazzi P, Neri G. Quantitative analysis of DNA demethylation and transcriptional reactivation of the FMR1 gene in fragile X cells treated with 5-azadeoxycytidine. Nucleic Acids Res 2002; 30:3278-85. [PMID: 12136110 PMCID: PMC135754 DOI: 10.1093/nar/gkf434] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In fragile X syndrome, hypermethylation of the expanded CGG repeat and of the upstream promoter leads to transcriptional silencing of the FMR1 gene. Absence of the FMR1 protein results in mental retardation. We previously proved that treatment with 5-azadeoxycytidine (5-azadC) of fragile X cell lines results in reactivation of the FMR1 gene. We now show that this treatment causes passive demethylation of the FMR1 gene promoter. We employed the bisulfite-sequencing technique to detect the methylation status of individual CpG sites in the entire promoter region, upstream of the CGG repeat. Lymphoblastoid cell lines of fragile X males with full mutations of different sizes were tested before and after treatment with 5-azadC at various time points. We observed that individual cells are either completely unmethylated or not, with few relevant exceptions. We also investigated the extent of methylation in the full mutation (CGG repeat) itself by Southern blot analysis after digestion with methylation-sensitive enzymes Fnu4HI and McrBC and found that the CGG repeat remains at least partially methylated in many cells with a demethylated promoter. This may explain the quantitative discrepancy between the large extent of promoter demethylation and the limited levels of FMR1 transcriptional reactivation estimated by quantitative real-time fluorescent RT-PCR analysis.
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Affiliation(s)
- Roberta Pietrobono
- Istituto di Genetica Medica, Università Cattolica, and Centro Ricerche per la Disabilità Mentale e Motoria, Associazione Anni Verdi, Largo F. Vito 1, 00168 Rome, Italy
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41
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42
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Bonifati V, De Michele G, Lücking CB, Dürr A, Fabrizio E, Ambrosio G, Vanacore N, De Mari M, Marconi R, Capus L, Breteler MM, Gasser T, Oostra B, Wood N, Agid Y, Filla A, Meco G, Brice A. The parkin gene and its phenotype. Italian PD Genetics Study Group, French PD Genetics Study Group and the European Consortium on Genetic Susceptibility in Parkinson's Disease. Neurol Sci 2001; 22:51-2. [PMID: 11487197 DOI: 10.1007/s100720170042] [Citation(s) in RCA: 26] [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] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Mutations of the parkin gene on chromosome 6 cause autosomal recessive, early onset parkinsonism. This is the most frequent form of monogenic parkinsonism so far identified. The associated phenotypical spectrum encompasses early onset, levodopa-responsive parkinsonism (average onset in the early 30s in Europe), and it overlaps with dopa-responsive dystonia in cases with the earliest onset, and with clinically typical Parkinson's disease in cases with later onset. Despite clinical features, Lewy bodies are not found at autopsy in brains of patients with parkin mutations. The parkin protein possesses ubiquitin ligase activity, which is abolished by the pathogenic mutations.
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Affiliation(s)
- V Bonifati
- Department of Neurological Sciences, La Sapienza University, Rome, Italy
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43
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Tunçbilek E, Alikasifoğlu M, Aktas D, Duman F, Yanik H, Anar B, Oostra B, Willemsen R. Screening for the fragile X syndrome among mentally retarded males by hair root analysis. Am J Med Genet 2000; 95:105-7. [PMID: 11078558 DOI: 10.1002/1096-8628(20001113)95:2<105::aid-ajmg3>3.0.co;2-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A noninvasive antibody test was used to identify male fragile X patients in special education schools, on the basis of the lack of FMRP in hair roots. We studied 300 males with mental retardation of unknown cause attending special schools. Patients were divided into two groups, based on the scores according to a fragile X check list (Group 1 </= 9 points and Group 2 >/= 10 points). Group 2 consists of 51 males and only 5 males in this group showed no FMRP expression in hair roots within the abnormal range (91%). Fragile X diagnosis in these cases was confirmed by DNA analysis. None of the males scoring more than 10 on the check list was diagnosed positive for the fragile X syndrome using DNA analysis. With our antibody test on hair roots we did not detect a fragile X patient in Group 1. The FMRP antibody test on hair roots is suitable in a screening program for the fragile X syndrome among mentally retarded males attending special education schools.
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Affiliation(s)
- E Tunçbilek
- Department of Pediatrics, Division of Medical Genetics, Hacettepe University, Ankara, Turkey.
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44
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Fryns JP, Borghgraef M, Brown TW, Chelly J, Fisch GS, Hamel B, Hanauer A, Lacombe D, Luo L, MacPherson JN, Mandel JL, Moraine C, Mulley J, Nelson D, Oostra B, Partington M, Ramakers GJ, Ropers HH, Rousseau F, Schwartz C, Steinbach P, Stoll C, Tranebjaerg L, Turner G, Van Bokhoven H, Vianna-Morgante A. 9th international workshop on fragile X syndrome and X-linked mental retardation. Am J Med Genet 2000; 94:345-60. [PMID: 11050616 DOI: 10.1002/1096-8628(20001023)94:5<345::aid-ajmg1>3.0.co;2-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- J P Fryns
- Clinical Genetics Unit/Center for Human Genetics, University Hospital of Leuven, Leuven, Belgium
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45
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Bonifati V, Joosse M, Nicholl DJ, Vanacore N, Bennett P, Rizzu P, Fabbrini G, Marconi R, Colosimo C, Locuratolo N, Stocchi F, Bonuccelli U, De Mari M, Wenning G, Vieregge P, Oostra B, Meco G, Heutink P. The tau gene in progressive supranuclear palsy: exclusion of mutations in coding exons and exon 10 splice sites, and identification of a new intronic variant of the disease-associated H1 haplotype in Italian cases. Neurosci Lett 1999; 274:61-5. [PMID: 10530520 DOI: 10.1016/s0304-3940(99)00669-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mutations in coding exons or exon 10 5'-splice-site of the gene for microtubule-associated protein tau can cause chromosome 17-linked frontotemporal dementia and parkinsonism (FTDP-17). We sequenced the 11 coding exons plus exon-intron boundaries of the tau gene in 15 cases of progressive supranuclear palsy (PSP), and found no mutations in coding exons or exon ten 5'-splice sites. These data indicate that typical PSP is not associated with tau gene mutations similar to those causing FTDP-17. We also observed a +39deltaG base change in the intron following exon 4 in three out of 69 PSP cases (all three Italians), whereas it was not found in 150 Dutch controls and once in 112 Italian controls. The +39deltaG variant arose in the context of the PSP-associated tau H1 haplotype. Although a pathogenic role cannot be entirely excluded, +39deltaG is likely to be a rare polymorphism that may be in linkage disequilibrium with a biologically relevant locus inside or near to the tau gene.
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Affiliation(s)
- V Bonifati
- Department of Neurosciences, La Sapienza University, Roma, Italy.
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46
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D'Adamo P, Menegon A, Lo Nigro C, Grasso M, Gulisano M, Tamanini F, Bienvenu T, Gedeon AK, Oostra B, Wu SK, Tandon A, Valtorta F, Balch WE, Chelly J, Toniolo D. Mutations in GDI1 are responsible for X-linked non-specific mental retardation. Nat Genet 1998; 19:134-9. [PMID: 9620768 DOI: 10.1038/487] [Citation(s) in RCA: 252] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rab GDP-dissociation inhibitors (GDI) are evolutionarily conserved proteins that play an essential role in the recycling of Rab GTPases required for vesicular transport through the secretory pathway. We have found mutations in the GDI1 gene (which encodes uGDI) in two families affected with X-linked non-specific mental retardation. One of the mutations caused a non-conservative substitution (L92P) which reduced binding and recycling of RAB3A, the second was a null mutation. Our results show that both functional and developmental alterations in the neuron may account for the severe impairment of learning abilities as a consequence of mutations in GDI1, emphasizing its critical role in development of human intellectual and learning abilities.
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Affiliation(s)
- P D'Adamo
- Institute of Genetics Biochemistry and Evolution, CNR, Pavia, Italy
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47
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Willemsen R, Los F, Mohkamsing S, van den Ouweland A, Deelen W, Galjaard H, Oostra B. Rapid antibody test for prenatal diagnosis of fragile X syndrome on amniotic fluid cells: a new appraisal. J Med Genet 1997; 34:250-1. [PMID: 9132500 PMCID: PMC1050903 DOI: 10.1136/jmg.34.3.250] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Fragile X syndrome is caused by mutations in the FMR1 gene and is one of the most frequent forms of inherited mental retardation in males. Postnatal and prenatal diagnosis of fragile X syndrome is feasible by direct DNA analysis. A new approach to prenatal diagnosis of fragile X syndrome in amniotic fluid cells is described, using a rapid and simple antibody test on uncultured amniotic fluid cells. The test requires 1 ml of amniotic fluid and the results of this antibody test are available on the same day as the amniocentesis.
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Affiliation(s)
- R Willemsen
- MGC-Department of Clinical Genetics, Erasmus University, Rotterdam, The Netherlands
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48
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Willemsen R, Bontekoe C, Tamanini F, Galjaard H, Hoogeveen A, Oostra B. Association of FMRP with ribosomal precursor particles in the nucleolus. Biochem Biophys Res Commun 1996; 225:27-33. [PMID: 8769090 DOI: 10.1006/bbrc.1996.1126] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The fragile X syndrome, one of the most common forms of inherited mental retardation, is caused by an expansion of a polymorphic CGG repeat upstream the coding region of the FMR1 gene. These expansions are associated with hypermethylation of the FMR1 gene, which results in the absence of the gene product, the FMR1 protein (FMRP). The physiological function of FMRP remains to be determined. We studied the ultrastructural localization of FMRP at the electron microscopical level using the immunogold technique. FMRP is associated with ribosomes attached to the endoplasmic reticulum and with ribosomes free in the cytoplasm. In addition, FMRP is found in the nucleus where the protein is associated with the granular component of the nucleolus. The cellular function of FMRP is hypothesized in relation to its subcellular distribution.
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Affiliation(s)
- R Willemsen
- MGC-Department of Clinical Genetics, Erasmus University, Rotterdam, The Netherlands
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49
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Tranebjaerg L, Lubs HA, Borghgraef M, Brown WT, Fisch G, Fryns JP, Hagerman R, Jacobs PA, Mandel JL, Mulley J, Oostra B, Schwartz C, Sherman S, Willard H, Willems P. Seventh International Workshop on the Fragile X and X-linked Mental Retardation. Am J Med Genet 1996; 64:1-14. [PMID: 8826442 DOI: 10.1002/(sici)1096-8628(19960712)64:1<1::aid-ajmg1>3.0.co;2-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- L Tranebjaerg
- Department of Medical Genetics, University Hospital of Tromsø, Norway
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50
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de Graaff E, Willemsen R, Zhong N, de Die-Smulders CE, Brown WT, Freling G, Oostra B. Instability of the CGG repeat and expression of the FMR1 protein in a male fragile X patient with a lung tumor. Am J Hum Genet 1995; 57:609-18. [PMID: 7668289 PMCID: PMC1801284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The molecular mechanism of the fragile X syndrome is based on the expansion of an CGG repeat in the 5' UTR of the FMR1 gene in the majority of fragile X patients. This repeat displays instability both between individuals and within an individual. We studied the instability of the CGG repeat and the expression of the FMR1 protein (FMRP) in several different tissues derived from a male fragile X patient. Using Southern blot analysis, only a full mutation is detected in 9 of the 11 tissues tested. The lung tumor contains a methylated premutation of 160 repeats, whereas in the testis, besides the full mutation, a premutation of 60 CGG repeats is detected. Immunohistochemistry of the testis revealed expression of FMR1 in the spermatogonia only, confirming the previous finding that, in the sperm cells of fragile X patients with a full mutation in their blood cells, only a premutation is present. Immunohistochemistry of brain and lung tissue revealed that 1% of the cells are expressing the FMRP. PCR analysis demonstrated the presence of a premutation of 160 repeats in these FMR1-expressing cells. This indicates that the tumor was derived from a lung cell containing a premutation. Remarkably, despite the methylation of the EagI and BssHII sites, FMRP expression is detected in the tumor. Methylation of both restriction sites has thus far resulted in a 100% correlation with the lack of FMR1 expression, but the results found in the tumor suggest that the CpGs in these restriction sites are not essential for regulation of FMR1 expression. This indicates a need for a more accurate study of the exact promoter of FMR1.
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Affiliation(s)
- E de Graaff
- Department of Clinical Genetics, Erasmus University, Rotterdam, The Netherlands
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