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      A comprehensive 1000 Genomes-based genome-wide association meta-analysis of coronary artery disease

      research-article
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          Abstract

          Existing knowledge of genetic variants affecting risk of coronary artery disease (CAD) is largely based on genome-wide association studies (GWAS) analysis of common SNPs. Leveraging phased haplotypes from the 1000 Genomes Project, we report a GWAS meta-analysis of 185 thousand CAD cases and controls, interrogating 6.7 million common (MAF>0.05) as well as 2.7 million low frequency (0.005<MAF<0.05) variants. In addition to confirmation of most known CAD loci, we identified 10 novel loci, eight additive and two recessive, that contain candidate genes that newly implicate biological processes in vessel walls. We observed intra-locus allelic heterogeneity but little evidence of low frequency variants with larger effects and no evidence of synthetic association. Our analysis provides a comprehensive survey of the fine genetic architecture of CAD showing that genetic susceptibility to this common disease is largely determined by common SNPs of small effect size.

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          Genomewide association analysis of coronary artery disease.

          Modern genotyping platforms permit a systematic search for inherited components of complex diseases. We performed a joint analysis of two genomewide association studies of coronary artery disease. We first identified chromosomal loci that were strongly associated with coronary artery disease in the Wellcome Trust Case Control Consortium (WTCCC) study (which involved 1926 case subjects with coronary artery disease and 2938 controls) and looked for replication in the German MI [Myocardial Infarction] Family Study (which involved 875 case subjects with myocardial infarction and 1644 controls). Data on other single-nucleotide polymorphisms (SNPs) that were significantly associated with coronary artery disease in either study (P 80%) of a true association: chromosomes 1p13.3 (rs599839), 1q41 (rs17465637), 10q11.21 (rs501120), and 15q22.33 (rs17228212). We identified several genetic loci that, individually and in aggregate, substantially affect the risk of development of coronary artery disease. Copyright 2007 Massachusetts Medical Society.
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            Rare Variants Create Synthetic Genome-Wide Associations

            Introduction Efforts to fine map the causal variants responsible for genome-wide association studies (GWAS) signals have been largely predicated on the common disease common variant theory, postulating a common variant as the culprit for observed associations. This has led to extensive resequencing efforts that have been largely unsuccessful [1]–[5]. Here, we explore the possibility that part of the reason for this may be that the disease class causing an observed association may consist of multiple low-frequency variants across large regions of the genome—a phenomenon we call synthetic association. For convenience, these less common variants will be referred to here as “rare,” but we emphasize that we use this term loosely, only to refer to variants less common than those routinely studied in GWAS. The basic idea of how synthetic associations emerge in this model is illustrated in Figure 1, which shows how rare variants, by chance, can occur disproportionately in some parts of a gene genealogy. Any variant “higher up in the genealogy” that partitions those parts of the genealogy containing more disease variants than average will be identified as disease-associated. It is well appreciated that a noncausal variant will show association with a causal variant if the two are in strong linkage disequilibrium (LD). We use the previously introduced term synthetic association [6], however, to describe how such indirect association can occur between a common variant and at least one and possibly many rarer causal variants. Using the term synthetic as opposed to indirect emphasizes that the properties of the association signal are very different when the responsible variant or variants are much less frequent than the marker that carries the signal, as we detail below. 10.1371/journal.pbio.1000294.g001 Figure 1 Example genealogies showing causal variants and the strongest association for a common variant. (A) A genealogy with 10,000 original haplotypes was generated with 3,000 cases and 3,000 controls, genotype relative risk (γ) = 4, and nine causal variants. The branches containing the strongest synthetic association are indicated in blue. The branches containing the rare causal variants are in red. (B) A second genealogy was generated using the same parameters. These genealogies demonstrate two scenarios with genome-wide significant synthetic associations: the first (upper genealogy) had a high risk allele frequency (RAF = 0.49), and the second (lower genealogy) had a low RAF (0.08). To assess the tendency of rare disease-causing variants to create synthetic signals of association that are credited to single polymorphisms that are much more common in the population than the causal variants, we have simulated 10,000 haplotypes based on a coalescent model in a region either with or without recombination (Materials and Methods). We assumed that gene variants that influence disease have an allele frequency between 0.005 and 0.02, which is generally below the range of reliable detection (either by inclusion or indirect representation) using the genome-wide association platforms currently in use. We assumed a baseline probability of disease of φ for individuals with none of the rare genetic risk factors. The presence of at least one rare risk allele at the locus increased the probability of disease from φ to γ. We considered two values of φ (0.01, 0.1) and chose values of the penetrance γ such that the genotypic relative risk (GRR) of the rare causal variants varied incrementally between 2 and 6, where GRR is the ratio γ/φ. These values were chosen to explore the space around a GRR of 4, a threshold above which consistent linkage signals would be expected [7]. We simulated scenarios with one, three, five, seven, and nine rare causal variants. Results Across the conditions we have studied, not only is it possible to achieve genome-wide significance for common variants when one or more rare variants are the only contributors to disease, it is often the likely outcome (Figure 2). Overall, 30% of the simulations were able to detect an association with a common SNP at genome-wide significance (p 5%, Hardy-Weinberg equilibrium p-value >1×10−6, SNP call rate >95%), using the PLINK software [40]. For the sickle cell anemia GWAS, we compared 194 cases and 7,407 controls of inferred African ancestry via multidimensional scaling, with a genomic control inflation factor of 1.01. For hearing loss, we performed a GWAS on 418 cases and 6,892 control subjects, all of whom were of genetically inferred European ancestry via multidimensional scaling, with a genomic control inflation factor of 1.02.
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              REST: a mammalian silencer protein that restricts sodium channel gene expression to neurons.

              Expression of the type II voltage-dependent sodium channel gene is restricted to neurons by a silencer element active in nonneuronal cells. We have cloned cDNA coding for a transcription factor (REST) that binds to this silencer element. Expression of a recombinant REST protein confers the ability to silence type II reporter genes in neuronal cell types lacking the native REST protein, whereas expression of a dominant negative form of REST in nonneuronal cells relieves silencing mediated by the native protein. REST transcripts in developing mouse embryos are detected ubiquitously outside of the nervous system. We propose that expression of the type II sodium channel gene in neurons reflects a default pathway that is blocked in nonneuronal cells by the presence of REST.
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                Author and article information

                Journal
                9216904
                2419
                Nat Genet
                Nat. Genet.
                Nature genetics
                1061-4036
                1546-1718
                27 August 2015
                07 September 2015
                October 2015
                01 April 2016
                : 47
                : 10
                : 1121-1130
                Affiliations
                [1 ]Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Canada
                [2 ]Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
                [3 ]Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
                [4 ]Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
                [5 ]Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA
                [6 ]Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
                [7 ]Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
                [8 ]Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
                [9 ]Institut für Integrative und Experimentelle Genomik, Universität zu Lübeck, Lübeck, Germany
                [10 ]DZHK (German Research Center for Cardiovascular Research) partner site Hamburg-Lübeck-Kiel, Lübeck, Germany
                [11 ]William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
                [12 ]Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
                [13 ]Center for Non-Communicable Diseases, Karachi, Pakistan
                [14 ]NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, UK
                [15 ]CTSU, Nuffield Department of Population Health, University of Oxford, Oxford, UK
                [16 ]Deutsches Herzzentrum München, Technische Universität München, München, Germany
                [17 ]DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, München, Germany
                [18 ]Department of Epidemiology, Erasmus University Medical center, Rotterdam, The Netherlands
                [19 ]Estonian Genome Center, University of Tartu, Tartu, Estonia
                [20 ]Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
                [21 ]Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
                [22 ]Department of Health, National Institute for Health and Welfare, Helsinki, Finland
                [23 ]Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
                [24 ]Diabetes & Obesity Research Program, University of Helsinki, Helsinki, Finland
                [25 ]Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
                [26 ]Harvard Medical School, Boston, Massachusetts, USA
                [27 ]State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center of Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
                [28 ]Robertson Center for Biostatistics, University of Glasgow, Glasgow, UK
                [29 ]Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
                [30 ]Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
                [31 ]Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
                [32 ]Molecular Epidemiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
                [33 ]Science for Life Laboratory, Uppsala University, Uppsala, Sweden
                [34 ]Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
                [35 ]National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, Massachusetts, USA
                [36 ]Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
                [37 ]Center for Genome Science, Korea National Institute of Health, Chungcheongbuk-do, Korea
                [38 ]Vth Department of Medicine (Nephrology, Hypertensiology, Endocrinology, Diabetology, Rheumatology), Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany
                [39 ]The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, New York, USA
                [40 ]The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, New York, USA
                [41 ]Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
                [42 ]Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere, Finland
                [43 ]Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
                [44 ]Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
                [45 ]Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, California, USA
                [46 ]Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
                [47 ]Institute for Medical Informatics, Statistics and Epidemiology, Medical Faculty, University of Leipzig, Leipzig, Germany
                [48 ]LIFE Research Center of Civilization Diseases, Leipzig, Germany
                [49 ]Icelandic Heart Association, Kopavogur, Iceland
                [50 ]Faculty of Medicine, University of Iceland, Reykjavik, Iceland
                [51 ]Department of Public Health, University of Helsinki, Helsinki, Finland
                [52 ]Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
                [53 ]Department of Epidemiology and Biostatistics, Imperial College London, London, UK
                [54 ]Department of Cardiology, Ealing Hospital NHS Trust, Middlesex, UK
                [55 ]Medical Research Institute, University of Dundee, Dundee, UK
                [56 ]Population Health Research Institute, Hamilton Health Sciences, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
                [57 ]Platform for Genome Analytics, Institutes of Neurogenetics & Integrative and Experimental Genomics, University of Lübeck, Lübeck, Germany
                [58 ]Neuroepidemiology and Ageing Research Unit, School of Public Health, Faculty of Medicine, The Imperial College of Science, Technology, and Medicine, London, UK
                [59 ]Heart Center Leipzig, Cardiology, University of Leipzig, Leipzig, Germany
                [60 ]Department of Dietetics-Nutrition, Harokopio University, Athens, Greece
                [61 ]INSERM, UMRS1138, Centre de Recherche des Cordeliers, Paris, France
                [62 ]Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, UK
                [63 ]Lebanese American University, School of Medicine, Beirut, Lebanon
                [64 ]Hypertension Division, Fuwai Hospital, National Center For Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
                [65 ]Klinikum rechts der Isar, München, Germany
                [66 ]Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Lübeck, Germany
                [67 ]Department of Public Health and Caring Sciences, Geriatrics, Uppsala University, Uppsala, Sweden
                [68 ]Institut für Epidemiologie, Christian-Albrechts Universität zu Kiel, Kiel, Germany
                [69 ]Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University, Uppsala, Sweden
                [70 ]Transplantation Laboratory, Haartman Institute, University of Helsinki, Helsinki, Finland
                [71 ]Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
                [72 ]Punjab Institute of Cardiology, Lahore, Pakistan
                [73 ]All India Institute of Medical Sciences, New Delhi, India
                [74 ]Institut für Humangenetik, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
                [75 ]Institute of Human Genetics, Technische Universität München, München, Germany
                [76 ]Red Crescent Institute of Cardiology, Hyderabad, Pakistan
                [77 ]Department of Biostatistics, University of Liverpool, Liverpool, UK
                [78 ]Department of Medicine, Department of Cardiology, Helsinki University Central Hospital, Helsinki, Finland
                [79 ]Second Department of Cardiology, Attikon Hospital, School of Medicine, University of Athens, Athens, Greece
                [80 ]Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
                [81 ]Department of Haematology, University of Cambridge, Cambridge, UK
                [82 ]Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
                [83 ]Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
                [84 ]National Human Genome Center at Beijing, Beijing, China
                [85 ]National Institue of Cardiovascular Diseases, Karachi, Pakistan
                [86 ]Division of Cardiology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
                [87 ]Associazione per lo Studio della Trombosi in Cardiologia, Pavia, Italy
                [88 ]Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
                [89 ]Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
                [90 ]Imperial College Healthcare NHS Trust, London, UK
                [91 ]Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
                [92 ]The Berlin Aging Study II; Research Group on Geriatrics; Charité - Universitätsmedizin Berlin, Berlin, Germany
                [93 ]Institute of Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
                [94 ]Grupo de Epidemiología y Genética Cardiovascular, Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona, Spain
                [95 ]MedStar Heart and Vascular Institute, MedStar Washington Hospital Center, Washington, DC, USA
                [96 ]Division of Endocrinology and Basic and Translational Obesity Research, Boston Children’s Hospital, Boston, Massachusetts, USA
                [97 ]Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
                [98 ]Department of Cardiovascular Research, IRCCS Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
                [99 ]Leeds Institute of Genetics, Health and Therapeutics, University of Leeds, Leeds, UK
                [100 ]Cardiovascular Genetics and Genomics Group, Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
                [101 ]Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
                [102 ]Cleveland Clinic, Cleveland, Ohio, USA
                [103 ]Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
                [104 ]Kaiser Permanente Division of Research, Oakland, California, USA
                [105 ]Durrer Center for Cardiogenetic Research, Amsterdam, The Netherlands
                [106 ]Interuniversity Cardiology Institute of the Netherlands, Utrecht, The Netherlands
                [107 ]Department of Forensic Medicine, University of Tampere School of Medicine, Tampere, Finland
                [108 ]Cardiovascular Science, National Heart and Lung Institute, Imperial College London, London, UK
                [109 ]Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
                [110 ]The Mindich Child Health and Development Institute, The Icahn School of Medicine at Mount Sinai, New York, New York, USA
                [111 ]Department of Clinical Sciences, Hypertension and Cardiovascular Disease, Lund University, University Hospital Malmö, Malmö, Sweden
                [112 ]Synlab Academy, Synlab Services GmbH, Mannheim, Germany
                [113 ]Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
                [114 ]Stanford Cardiovascular Institute, Stanford University, Stanford, California, USA
                [115 ]Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
                [116 ]Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
                [117 ]University of Ottawa Heart Institute, Ottawa, Canada
                [118 ]Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
                [119 ]Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
                [120 ]Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
                [121 ]Oklahoma Center for Neuroscience, Oklahoma City, Oklahoma, USA
                [122 ]Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
                [123 ]Department of Epidemiology, University of Washington, Seattle, Washington, USA
                [124 ]Department of Prosthetic Dentistry, Center for Dental and Oral Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
                [125 ]Institute of Cardiovascular and Medical Sciences, Faculty of Medicine, University of Glasgow, Glasgow, UK
                [126 ]Institute for Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Medical Faculty, Leipzig, Germany
                [127 ]Harvard School of Public Health, Boston, Massachusetts, USA
                [128 ]National Heart, Lung and Blood Institute Division of Intramural Research, Bethesda, Maryland, USA
                [129 ]Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts, USA
                [130 ]Department of Health Sciences, University of Leicester, Leicester, UK
                [131 ]Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
                Author notes
                [133]

                These authors jointly supervised this work.

                Article
                EMS64693
                10.1038/ng.3396
                4589895
                26343387
                13105be2-901c-499f-8b8a-57f9fc5b0747

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