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He KY, Kelly TN, Wang H, Liang J, Zhu L, Cade BE, Assimes TL, Becker LC, Beitelshees AL, Bielak LF, Bress AP, Brody JA, Chang YPC, Chang YC, de Vries PS, Duggirala R, Fox ER, Franceschini N, Furniss AL, Gao Y, Guo X, Haessler J, Hung YJ, Hwang SJ, Irvin MR, Kalyani RR, Liu CT, Liu C, Martin LW, Montasser ME, Muntner PM, Mwasongwe S, Naseri T, Palmas W, Reupena MS, Rice KM, Sheu WHH, Shimbo D, Smith JA, Snively BM, Yanek LR, Zhao W, Blangero J, Boerwinkle E, Chen YDI, Correa A, Cupples LA, Curran JE, Fornage M, He J, Hou L, Kaplan RC, Kardia SLR, Kenny EE, Kooperberg C, Lloyd-Jones D, Loos RJF, Mathias RA, McGarvey ST, Mitchell BD, North KE, Peyser PA, Psaty BM, Raffield LM, Rao DC, Redline S, Reiner AP, Rich SS, Rotter JI, Taylor KD, Tracy R, Vasan RS, Morrison AC, Levy D, Chakravarti A, Arnett DK, Zhu X. Rare coding variants in RCN3 are associated with blood pressure. BMC Genomics 2022; 23:148. [PMID: 35183128 PMCID: PMC8858539 DOI: 10.1186/s12864-022-08356-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/17/2021] [Accepted: 02/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While large genome-wide association studies have identified nearly one thousand loci associated with variation in blood pressure, rare variant identification is still a challenge. In family-based cohorts, genome-wide linkage scans have been successful in identifying rare genetic variants for blood pressure. This study aims to identify low frequency and rare genetic variants within previously reported linkage regions on chromosomes 1 and 19 in African American families from the Trans-Omics for Precision Medicine (TOPMed) program. Genetic association analyses weighted by linkage evidence were completed with whole genome sequencing data within and across TOPMed ancestral groups consisting of 60,388 individuals of European, African, East Asian, Hispanic, and Samoan ancestries. RESULTS Associations of low frequency and rare variants in RCN3 and multiple other genes were observed for blood pressure traits in TOPMed samples. The association of low frequency and rare coding variants in RCN3 was further replicated in UK Biobank samples (N = 403,522), and reached genome-wide significance for diastolic blood pressure (p = 2.01 × 10- 7). CONCLUSIONS Low frequency and rare variants in RCN3 contributes blood pressure variation. This study demonstrates that focusing association analyses in linkage regions greatly reduces multiple-testing burden and improves power to identify novel rare variants associated with blood pressure traits.
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Affiliation(s)
- Karen Y He
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road, Cleveland, OH, 44106, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Heming Wang
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Jingjing Liang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road, Cleveland, OH, 44106, USA
| | - Luke Zhu
- Center for Human Genetics & Genomics, New York University Grossman School of Medicine, New York, NY, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Themistocles L Assimes
- Department of Medicine (Division of Cardiovascular Medicine), Stanford University, Palo Alto, CA, USA
| | - Lewis C Becker
- GeneSTAR Research Program, Department of Medicine, Divisions of Cardiology and General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amber L Beitelshees
- Division of Endocrinology, Diabetes, and Nutrition, Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Adam P Bress
- Department of Population Health Sciences, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Yen-Pei Christy Chang
- Division of Endocrinology, Diabetes, and Nutrition, Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yi-Cheng Chang
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei City, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Ervin R Fox
- Division of Cardiovascular Diseases, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Nora Franceschini
- Department of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Anna L Furniss
- Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
| | - Yan Gao
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Yi-Jen Hung
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, Taiwan
| | - Shih-Jen Hwang
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
- Framingham Heart Study, National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
| | - Marguerite Ryan Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AB, USA
| | - Rita R Kalyani
- GeneSTAR Research Program, Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ching-Ti Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
- Framingham Heart Study, National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
| | - Chunyu Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
- Framingham Heart Study, National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
| | - Lisa Warsinger Martin
- Division of Cardiology, Department of Medicine, George Washington University, Washington, DC, USA
| | - May E Montasser
- Division of Endocrinology, Diabetes, and Nutrition, Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Paul M Muntner
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AB, USA
| | | | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - Walter Palmas
- Division of Cardiology, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Kenneth M Rice
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Wayne H-H Sheu
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung City, Taiwan
| | - Daichi Shimbo
- Division of Cardiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Beverly M Snively
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Department of Medicine, Division of General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
- Division of Genomic Outcomes, Department of Pediatrics, Harbor-UCLA Medical Center Professor of Pediatrics, UCLA, Torrance, CA, USA
| | - Adolfo Correa
- Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
| | - L Adrienne Cupples
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
- Framingham Heart Study, National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University Chicago, Evanston, IL, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Donald Lloyd-Jones
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rasika A Mathias
- GeneSTAR Research Program, Department of Medicine, Divisions of Allergy and Clinical Immunology and General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephen T McGarvey
- International Health Institute and Department of Epidemiology, School of Public Health, Brown University, Providence, RI, USA
- Department of Anthropology, Brown University, Providence, RI, USA
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes, and Nutrition, Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Veterans Affairs Medical Center, Baltimore, MD, USA
| | - Kari E North
- Department of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - D C Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Russell Tracy
- Department of Pathology & Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | - Ramachandran S Vasan
- Framingham Heart Study, National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
- Department of Medicine, School of Medicine, Boston University, Boston, MA, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Daniel Levy
- Framingham Heart Study, National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Aravinda Chakravarti
- Center for Human Genetics & Genomics, New York University Grossman School of Medicine, New York, NY, USA
| | - Donna K Arnett
- University of Kentucky College of Public Health, Lexington, KY, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road, Cleveland, OH, 44106, USA.
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