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Iwaki H, Blauwendraat C, Leonard HL, Kim JJ, Liu G, Maple-Grødem J, Corvol JC, Pihlstrøm L, van Nimwegen M, Hutten SJ, Nguyen KDH, Rick J, Eberly S, Faghri F, Auinger P, Scott KM, Wijeyekoon R, Van Deerlin VM, Hernandez DG, Gibbs JR, Chitrala KN, Day-Williams AG, Brice A, Alves G, Noyce AJ, Tysnes OB, Evans JR, Breen DP, Estrada K, Wegel CE, Danjou F, Simon DK, Andreassen O, Ravina B, Toft M, Heutink P, Bloem BR, Weintraub D, Barker RA, Williams-Gray CH, van de Warrenburg BP, Van Hilten JJ, Scherzer CR, Singleton AB, Nalls MA. Genomewide association study of Parkinson's disease clinical biomarkers in 12 longitudinal patients' cohorts. Mov Disord 2019; 34:1839-1850. [PMID: 31505070 PMCID: PMC7017876 DOI: 10.1002/mds.27845] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/17/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Several reports have identified different patterns of Parkinson's disease progression in individuals carrying missense variants in GBA or LRRK2 genes. The overall contribution of genetic factors to the severity and progression of Parkinson's disease, however, has not been well studied. OBJECTIVES To test the association between genetic variants and the clinical features of Parkinson's disease on a genomewide scale. METHODS We accumulated individual data from 12 longitudinal cohorts in a total of 4093 patients with 22,307 observations for a median of 3.81 years. Genomewide associations were evaluated for 25 cross-sectional and longitudinal phenotypes. Specific variants of interest, including 90 recently identified disease-risk variants, were also investigated post hoc for candidate associations with these phenotypes. RESULTS Two variants were genomewide significant. Rs382940(T>A), within the intron of SLC44A1, was associated with reaching Hoehn and Yahr stage 3 or higher faster (hazard ratio 2.04 [1.58-2.62]; P value = 3.46E-8). Rs61863020(G>A), an intergenic variant and expression quantitative trait loci for α-2A adrenergic receptor, was associated with a lower prevalence of insomnia at baseline (odds ratio 0.63 [0.52-0.75]; P value = 4.74E-8). In the targeted analysis, we found 9 associations between known Parkinson's risk variants and more severe motor/cognitive symptoms. Also, we replicated previous reports of GBA coding variants (rs2230288: p.E365K; rs75548401: p.T408M) being associated with greater motor and cognitive decline over time, and an APOE E4 tagging variant (rs429358) being associated with greater cognitive deficits in patients. CONCLUSIONS We identified novel genetic factors associated with heterogeneity of Parkinson's disease. The results can be used for validation or hypothesis tests regarding Parkinson's disease. © 2019 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Hirotaka Iwaki
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
- Data Tecnica International, Glen Echo, Maryland, USA
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Hampton L. Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
- Data Tecnica International, Glen Echo, Maryland, USA
| | - Jonggeol J. Kim
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Ganqiang Liu
- School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Center for Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Precision Neurology Program, Harvard Medical School, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Jodi Maple-Grødem
- The Norwegian Centre for Movement Disorders, Stavanger University Hospital, Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Engineering, University in Stavanger, Stavanger, Norway
| | - Jean-Christophe Corvol
- Assistance-Publique Hôpitaux de Paris, ICM, INSERM UMRS 1127, CNRS 7225, ICM, Department of Neurology and CIC Neurosciences, Pitié-Salpêtrière Hospital, Paris, France
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Marlies van Nimwegen
- Radboud University Medical Centre, Donders Institute for Brain, Cognition, and Behaviour; Department of Neurology, Nijmegen, The Netherlands
| | - Samantha J. Hutten
- The Michael J. Fox Foundation for Parkinson’s Research, New York, New York, USA
| | | | - Jacqueline Rick
- Department of Neurology University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Shirley Eberly
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, New York, USA
| | - Faraz Faghri
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
- Department of Computer Science, University of Illinois Urbana-Champaign, Champaign, Illinois, USA
| | - Peggy Auinger
- Department of Neurology, Center for Health + Technology, University of Rochester, Rochester, New York, USA
| | - Kirsten M. Scott
- Department of Clinical Neurosciences, University of Cambridge, John van Geest Centre for Brain Repair, Cambridge, United Kingdom
| | - Ruwani Wijeyekoon
- Department of Clinical Neurosciences, University of Cambridge, John van Geest Centre for Brain Repair, Cambridge, United Kingdom
| | - Vivianna M. Van Deerlin
- Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Disease Research, Parelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dena G. Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - J. Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Kumaraswamy Naidu Chitrala
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Aaron G. Day-Williams
- Flagship Labs 60 Inc, Cambridge, Massachusetts, USA
- Statistical Genetics, Biogen, Cambridge, Massachusetts, USA
| | - Alexis Brice
- Institut du cerveau et de la moelle épinière ICM, Paris, France
- Sorbonne Université SU, Paris, France
- INSERM UMR1127, Paris, France
| | - Guido Alves
- The Norwegian Centre for Movement Disorders, Stavanger University Hospital, Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Engineering, University in Stavanger, Stavanger, Norway
- Department of Neurology, Stavanger University Hospital, Stavanger, Norway
| | - Alastair J. Noyce
- Preventive Neurology Unit, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, United Kingdom
- Department of Clinical and Movement Neurosciences, UCL Institute of Neurology, London, United Kingdom
| | - Ole-Bjørn Tysnes
- Department of Neurology, Haukeland University Hospital, Bergen, Norway
- University of Bergen, Bergen, Norway
| | - Jonathan R. Evans
- Department of Neurology, Nottingham University NHS Trust, Nottingham, United Kingdom
| | - David P. Breen
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, Scotland
- Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, Scotland
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland
| | - Karol Estrada
- Translational Genome Sciences, Biogen, Cambridge, Massachusetts, USA
| | - Claire E. Wegel
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana, USA
| | - Fabrice Danjou
- Institut du cerveau et de la moelle épinière ICM, Paris, France
| | - David K. Simon
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Ole Andreassen
- NORMENT, Institute of Clinical Medicine, University of Oslo, Oslo, Norway, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway, Norway
| | - Bernard Ravina
- Voyager Therapeutics, Cambridge, Massachusetts, USA
- Department of Neurology, University of Rochester School of Medicine, Rochester, New York, USA
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Peter Heutink
- German Center for Neurodegenerative Diseases-Tubingen, Tuebingen, Germany
- HIH Tuebingen, Tubingen, Tuebingen, Germany
| | - Bastiaan R. Bloem
- Radboud University Medical Centre, Donders Institute for Brain, Cognition, and Behaviour; Department of Neurology, Nijmegen, The Netherlands
| | - Daniel Weintraub
- Department of Psychiatry, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
- Department of Veterans Affairs, Philadelphia, Pennsylvania, USA
| | - Roger A. Barker
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | | | - Bart P. van de Warrenburg
- Radboud University Medical Centre, Donders Institute for Brain, Cognition, and Behaviour; Department of Neurology, Nijmegen, The Netherlands
| | | | - Clemens R. Scherzer
- Advanced Center for Parkinson’s Disease Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Precision Neurology Program, Harvard Medical School, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Andrew B. Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Mike A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
- Data Tecnica International, Glen Echo, Maryland, USA
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Gong J, Nishimura KK, Fernandez-Rhodes L, Haessler J, Bien S, Graff M, Lim U, Lu Y, Gross M, Fornage M, Yoneyama S, Isasi CR, Buzkova P, Daviglus M, Lin DY, Tao R, Goodloe R, Bush WS, Farber-Eger E, Boston J, Dilks HH, Ehret G, Gu CC, Lewis CE, Nguyen KDH, Cooper R, Leppert M, Irvin MR, Bottinger EP, Wilkens LR, Haiman CA, Park L, Monroe KR, Cheng I, Stram DO, Carlson CS, Jackson R, Kuller L, Houston D, Kooperberg C, Buyske S, Hindorff LA, Crawford DC, Loos RJ, Le Marchand L, Matise TC, North KE, Peters U. Trans-ethnic analysis of metabochip data identifies two new loci associated with BMI. Int J Obes (Lond) 2018; 42:384-390. [PMID: 29381148 PMCID: PMC5876082 DOI: 10.1038/ijo.2017.304] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 11/03/2017] [Accepted: 11/21/2017] [Indexed: 01/05/2023]
Abstract
OBJECTIVE Body mass index (BMI) is commonly used to assess obesity, which is associated with numerous diseases and negative health outcomes. BMI has been shown to be a heritable, polygenic trait, with close to 100 loci previously identified and replicated in multiple populations. We aim to replicate known BMI loci and identify novel associations in a trans-ethnic study population. SUBJECTS Using eligible participants from the Population Architecture using Genomics and Epidemiology consortium, we conducted a trans-ethnic meta-analysis of 102 514 African Americans, Hispanics, Asian/Native Hawaiian, Native Americans and European Americans. Participants were genotyped on over 200 000 SNPs on the Illumina Metabochip custom array, or imputed into the 1000 Genomes Project (Phase I). Linear regression of the natural log of BMI, adjusting for age, sex, study site (if applicable), and ancestry principal components, was conducted for each race/ethnicity within each study cohort. Race/ethnicity-specific, and combined meta-analyses used fixed-effects models. RESULTS We replicated 15 of 21 BMI loci included on the Metabochip, and identified two novel BMI loci at 1q41 (rs2820436) and 2q31.1 (rs10930502) at the Metabochip-wide significance threshold (P<2.5 × 10-7). Bioinformatic functional investigation of SNPs at these loci suggests a possible impact on pathways that regulate metabolism and adipose tissue. CONCLUSION Conducting studies in genetically diverse populations continues to be a valuable strategy for replicating known loci and uncovering novel BMI associations.
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Affiliation(s)
- Jian Gong
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Katherine K. Nishimura
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Lindsay Fernandez-Rhodes
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffery Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Stephanie Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Misa Graff
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Unhee Lim
- Cancer Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Myron Gross
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Myriam Fornage
- Health Science Center, University of Texas, Austin, Texas, United States of America
| | - Sachiko Yoneyama
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Carmen R. Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Petra Buzkova
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Martha Daviglus
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, U United States of America SA
| | - Dan-Yu Lin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ran Tao
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Robert Goodloe
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - William S. Bush
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Eric Farber-Eger
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jonathan Boston
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Holli H. Dilks
- Sarah Cannon Research Institute, Nashville, Tennessee, United States of America
| | - Georg Ehret
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Division of Cardiology, Geneva University Hospital, Geneva, Switzerland
| | - C. Charles Gu
- Department of Biostatistics, Washington University, St. Louis, Missouri, United States of America
| | - Cora E. Lewis
- Department of Medicine, University of Alabama, Birmingham, Alabama, United States of America
| | - Khanh-Dung H. Nguyen
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Richard Cooper
- Preventive Medicine and Epidemiology, Loyola University, Chicago, Illinois, United States of America
| | - Mark Leppert
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama, Birmingham, Alabama, United States of America
| | - Erwin P. Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Lynne R. Wilkens
- Cancer Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Christopher A. Haiman
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Lani Park
- Cancer Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Kristine R. Monroe
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont, California, United States of America
| | - Daniel O. Stram
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Christopher S. Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Rebecca Jackson
- Department of Internal Medicine, Ohio State Medical Center, Columbus, Ohio, United States of America
| | - Lew Kuller
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Denise Houston
- Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Steven Buyske
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
- Department of Statistics and Biostatistics, Rutgers University, Piscataway, New Jersey, United States of America
| | - Lucia A. Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Dana C. Crawford
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Loic Le Marchand
- Cancer Research Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Tara C. Matise
- Department of Genetics, Rutgers University, Piscataway, New Jersey, United States of America
| | - Kari E. North
- Department of Epidemiology, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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3
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Yoneyama S, Yao J, Guo X, Fernandez-Rhodes L, Lim U, Boston J, Buzková P, Carlson CS, Cheng I, Cochran B, Cooper R, Ehret G, Fornage M, Gong J, Gross M, Gu CC, Haessler J, Haiman CA, Henderson B, Hindorff LA, Houston D, Irvin MR, Jackson R, Kuller L, Leppert M, Lewis CE, Li R, Le Marchand L, Matise TC, Nguyen KDH, Chakravarti A, Pankow JS, Pankratz N, Pooler L, Ritchie MD, Bien SA, Wassel CL, Chen YDI, Taylor KD, Allison M, Rotter JI, Schreiner PJ, Schumacher F, Wilkens L, Boerwinkle E, Kooperberg C, Peters U, Buyske S, Graff M, North KE. Generalization and fine mapping of European ancestry-based central adiposity variants in African ancestry populations. Int J Obes (Lond) 2017; 41:324-331. [PMID: 27867202 PMCID: PMC5296276 DOI: 10.1038/ijo.2016.207] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 10/12/2016] [Accepted: 10/23/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND/OBJECTIVES Central adiposity measures such as waist circumference (WC) and waist-to-hip ratio (WHR) are associated with cardiometabolic disorders independently of body mass index (BMI) and are gaining clinically utility. Several studies report genetic variants associated with central adiposity, but most utilize only European ancestry populations. Understanding whether the genetic associations discovered among mainly European descendants are shared with African ancestry populations will help elucidate the biological underpinnings of abdominal fat deposition. SUBJECTS/METHODS To identify the underlying functional genetic determinants of body fat distribution, we conducted an array-wide association meta-analysis among persons of African ancestry across seven studies/consortia participating in the Population Architecture using Genomics and Epidemiology (PAGE) consortium. We used the Metabochip array, designed for fine-mapping cardiovascular-associated loci, to explore novel array-wide associations with WC and WHR among 15 945 African descendants using all and sex-stratified groups. We further interrogated 17 known WHR regions for African ancestry-specific variants. RESULTS Of the 17 WHR loci, eight single-nucleotide polymorphisms (SNPs) located in four loci were replicated in the sex-combined or sex-stratified meta-analyses. Two of these eight independently associated with WHR after conditioning on the known variant in European descendants (rs12096179 in TBX15-WARS2 and rs2059092 in ADAMTS9). In the fine-mapping assessment, the putative functional region was reduced across all four loci but to varying degrees (average 40% drop in number of putative SNPs and 20% drop in genomic region). Similar to previous studies, the significant SNPs in the female-stratified analysis were stronger than the significant SNPs from the sex-combined analysis. No novel associations were detected in the array-wide analyses. CONCLUSIONS Of 17 previously identified loci, four loci replicated in the African ancestry populations of this study. Utilizing different linkage disequilibrium patterns observed between European and African ancestries, we narrowed the suggestive region containing causative variants for all four loci.
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Affiliation(s)
- Sachiko Yoneyama
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Jie Yao
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | | | - Unhee Lim
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Jonathan Boston
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Petra Buzková
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Christopher S. Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Iona Cheng
- Cancer Prevention Institute of California, Fremont, CA, 94538, USA
| | - Barbara Cochran
- Baylor College of Medicine, Houston, TX, 77030, USA
- Division of Cardiology, Geneva University Hospital, Genève, 1205, Switzerland
| | - Richard Cooper
- Preventive Medicine and Epidemiology, Loyola University, Chicago, IL, 60153, USA
| | - Georg Ehret
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Myriam Fornage
- The Human Genetics Center and Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jian Gong
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Myron Gross
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - C. Charles Gu
- Department of Biostatistics, Washington University, St. Louis, MO, 63110, USA
| | - Jeff Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Christopher A. Haiman
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Brian Henderson
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Lucia A. Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Denise Houston
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Marguerite R. Irvin
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Rebecca Jackson
- Department of Internal Medicine, Ohio State Medical Center, Columbus, OH, 43210, USA
| | - Lew Kuller
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mark Leppert
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA
| | - Cora E. Lewis
- Department of Medicine, University of Alabama, Birmingham, AL, 35294, USA
| | - Rongling Li
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Tara C. Matise
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Khanh-Dung H. Nguyen
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Aravinda Chakravarti
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - James S. Pankow
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Nathan Pankratz
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Loreall Pooler
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Marylyn D. Ritchie
- Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA, 16801, USA
| | - Stephanie A. Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Christina L. Wassel
- University of Vermont College of Medicine, Department of Pathology and Laboratory Medicine, Colchester, VT, 05446, USA
| | - Yii-Der I. Chen
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Matthew Allison
- School of Medicine, University of California San Diego, Department of Preventive Medicine, San Diego, CA, 92110, USA
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Pamela J. Schreiner
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Fredrick Schumacher
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
| | - Lynne Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Eric Boerwinkle
- The Human Genetics Center and Institute of Molecular Medicine, Houston, TX, 77030, USA
- Department of Statistics and Biostatistics, Rutgers University, Piscataway, NJ, 8854, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Steven Buyske
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Kari E. North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27514, USA
- Carolina Center for Genome Sciences, Chapel Hill, NC, 27514, USA
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Nguyen KDH, Pihur V, Ganesh SK, Rakha A, Cooper RS, Hunt SC, Freedman BI, Coresh J, Kao WHL, Morrison AC, Boerwinkle E, Ehret GB, Chakravarti A. Effects of rare and common blood pressure gene variants on essential hypertension: results from the Family Blood Pressure Program, CLUE, and Atherosclerosis Risk in Communities studies. Circ Res 2013; 112:318-26. [PMID: 23149595 PMCID: PMC3548950 DOI: 10.1161/circresaha.112.276725] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
RATIONALE Hypertension affects ≈30% of adults in industrialized countries and is the major risk factor for cardiovascular disease. OBJECTIVE We sought to study the genetic effect of coding and conserved noncoding variants in syndromic hypertension genes on systolic blood pressure (BP) and diastolic BP to assess their overall impact on essential hypertension. METHODS AND RESULTS We resequenced 11 genes (AGT, CYP11B1, CYP17A1, HSD11B2, NR3C1, NR3C2, SCNN1A, SCNN1B, SCNN1G, WNK1, and WNK4) in 560 European American (EA) and African American ancestry GenNet participants with extreme systolic BP. We investigated genetic associations of 2535 variants with BP in 19997 EAs and in 6069 African Americans in 3 types of analyses. First, we studied the combined effects of all variants in GenNet. Second, we studied 1000 Genomes imputed polymorphic variants in 9747 EA and 3207 African American Atherosclerosis Risk in Communities subjects. Finally, we genotyped 37 missense and common noncoding variants in 6591 EAs and in 6521 individuals (3659 EA/2862 African American) from the CLUE and Family Blood Pressure Program studies, respectively. None of the variants individually reached significant false-discovery rates ≤0.05 for systolic BP and diastolic BP. However, on pooling all coding and noncoding variants, we identified at least 5 loci (AGT, CYP11B1, NR3C2, SCNN1G, and WNK1) with higher association at evolutionary conserved sites. CONCLUSIONS Both rare and common variants at these genes affect BP in the general population with modest effects sizes (<0.05 standard deviation units), and much larger sample sizes are required to assess the impact of individual genes. Collectively, conserved noncoding variants affect BP to a greater extent than missense mutations.
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Affiliation(s)
- Khanh-Dung H. Nguyen
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Pre-doctoral Training Program in Human Genetics and Molecular Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Vasyl Pihur
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Santhi K. Ganesh
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Ankit Rakha
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard S. Cooper
- Department of Community Medicine, Loyola University School of Medicine, Maywood, IL, USA
| | - Steven C. Hunt
- Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Joe Coresh
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Wen H. L. Kao
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Alanna C. Morrison
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Georg B. Ehret
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Cardiology, Department of Specialties of Internal Medicine, Geneva University Hospital, Geneva, Switzerland
| | - Aravinda Chakravarti
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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