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Blobner BM, Kirabo A, Kashlan OB, Sheng S, Arnett DK, Becker LC, Boerwinkle E, Carlson JC, Gao Y, Gibbs RA, He J, Irvin MR, Kardia SLR, Kelly TN, Kooperberg C, McGarvey ST, Menon VK, Montasser ME, Naseri T, Redline S, Reiner AP, Reupena MS, Smith JA, Sun X, Vaidya D, Viaud-Martinez KA, Weeks DE, Yanek LR, Zhu X, Minster RL, Kleyman TR. Rare Variants in Genes Encoding Subunits of the Epithelial Na + Channel Are Associated With Blood Pressure and Kidney Function. Hypertension 2022; 79:2573-2582. [PMID: 36193739 PMCID: PMC9669116 DOI: 10.1161/hypertensionaha.121.18513] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 07/31/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND The epithelial Na+ channel (ENaC) is intrinsically linked to fluid volume homeostasis and blood pressure. Specific rare mutations in SCNN1A, SCNN1B, and SCNN1G, genes encoding the α, β, and γ subunits of ENaC, respectively, are associated with extreme blood pressure phenotypes. No associations between blood pressure and SCNN1D, which encodes the δ subunit of ENaC, have been reported. A small number of sequence variants in ENaC subunits have been reported to affect functional transport in vitro or blood pressure. The effects of the vast majority of rare and low-frequency ENaC variants on blood pressure are not known. METHODS We explored the association of low frequency and rare variants in the genes encoding ENaC subunits, with systolic blood pressure, diastolic blood pressure, mean arterial pressure, and pulse pressure. Using whole-genome sequencing data from 14 studies participating in the Trans-Omics in Precision Medicine Whole-Genome Sequencing Program, and sequence kernel association tests. RESULTS We found that variants in SCNN1A and SCNN1B were associated with diastolic blood pressure and mean arterial pressure (P<0.00625). Although SCNN1D is poorly expressed in human kidney tissue, SCNN1D variants were associated with systolic blood pressure, diastolic blood pressure, mean arterial pressure, and pulse pressure (P<0.00625). ENaC variants in 2 of the 4 subunits (SCNN1B and SCNN1D) were also associated with estimated glomerular filtration rate (P<0.00625), but not with stroke. CONCLUSIONS Our results suggest that variants in extrarenal ENaCs, in addition to ENaCs expressed in kidneys, influence blood pressure and kidney function.
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Affiliation(s)
- Brandon M Blobner
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Annet Kirabo
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ossama B Kashlan
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shaohu Sheng
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Lewis C Becker
- GeneSTAR Research Program, Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eric Boerwinkle
- 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
| | - Jenna C Carlson
- Department of Biostatistics, University of Pittsburgh Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yan Gao
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Tulane University Translational Science Institute, New Orleans, LA, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sharon LR Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Tulane University Translational Science Institute, New Orleans, LA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephen T McGarvey
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI, USA
| | - Vipin K Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - May E Montasser
- Department of Medicine, University of Maryland, Baltimore, MD, USA
| | - Take Naseri
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI, USA
- Ministry of Health, Apia, Samoa
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Xiao Sun
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Dhananjay Vaidya
- GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Daniel E Weeks
- Department of Biostatistics, University of Pittsburgh Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - Ryan L Minster
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Thomas R Kleyman
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Cell Biology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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2
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Sikdar S, Joehanes R, Joubert BR, Xu CJ, Vives-Usano M, Rezwan FI, Felix JF, Ward JM, Guan W, Richmond RC, Brody JA, Küpers LK, Baïz N, Håberg SE, Smith JA, Reese SE, Aslibekyan S, Hoyo C, Dhingra R, Markunas CA, Xu T, Reynolds LM, Just AC, Mandaviya PR, Ghantous A, Bennett BD, Wang T, Consortium TBIOS, Bakulski KM, Melen E, Zhao S, Jin J, Herceg Z, van Meurs J, Taylor JA, Baccarelli AA, Murphy SK, Liu Y, Munthe-Kaas MC, Deary IJ, Nystad W, Waldenberger M, Annesi-Maesano I, Conneely K, Jaddoe VWV, Arnett D, Snieder H, Kardia SLR, Relton CL, Ong KK, Ewart S, Moreno-Macias H, Romieu I, Sotoodehnia N, Fornage M, Motsinger-Reif A, Koppelman GH, Bustamante M, Levy D, London SJ. Comparison of smoking-related DNA methylation between newborns from prenatal exposure and adults from personal smoking. Epigenomics 2019; 11:1487-1500. [PMID: 31536415 PMCID: PMC6836223 DOI: 10.2217/epi-2019-0066] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [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: 03/07/2019] [Accepted: 08/13/2019] [Indexed: 12/17/2022] Open
Abstract
Aim: Cigarette smoking influences DNA methylation genome wide, in newborns from pregnancy exposure and in adults from personal smoking. Whether a unique methylation signature exists for in utero exposure in newborns is unknown. Materials & methods: We separately meta-analyzed newborn blood DNA methylation (assessed using Illumina450k Beadchip), in relation to sustained maternal smoking during pregnancy (9 cohorts, 5648 newborns, 897 exposed) and adult blood methylation and personal smoking (16 cohorts, 15907 participants, 2433 current smokers). Results & conclusion: Comparing meta-analyses, we identified numerous signatures specific to newborns along with many shared between newborns and adults. Unique smoking-associated genes in newborns were enriched in xenobiotic metabolism pathways. Our findings may provide insights into specific health impacts of prenatal exposure on offspring.
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Affiliation(s)
- Sinjini Sikdar
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Roby Joehanes
- Hebrew SeniorLife, Harvard Medical School, Boston, MA 02115, USA
- Framingham Heart Study, Framingham, MA 01702, USA
| | - Bonnie R Joubert
- Department of Health & Human Services, Division of Extramural Research & Training, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Cheng-Jian Xu
- Department of Pediatric Pulmonology & Pediatric Allergology, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, PO Box 30001, Groningen, The Netherlands
- GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, PO Box 30001, Groningen, The Netherlands
| | - Marta Vives-Usano
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Center for Genomic Regulation (CRG), Barcelona Institute of Science & Technology, Barcelona, Spain
| | - Faisal I Rezwan
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Janine F Felix
- The Generation R Study Group, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - James M Ward
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
| | - Jennifer A Brody
- Department of Medicine, Epidemiology, & Health Services, Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98101, USA
| | - Leanne K Küpers
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Division of Human Nutrition & Health, Wageningen University, Wageningen, The Netherlands
| | - Nour Baïz
- Epidemiology of Allergic & Respiratory Diseases Department (EPAR), Sorbonne Universités, INSERM, Pierre Louis Institute of Epidemiology & Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Siri E Håberg
- Centre for Fertility & Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah E Reese
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Stella Aslibekyan
- College of Public Health, University of Kentucky, Lexington, KY 40536, USA
| | - Cathrine Hoyo
- Department of Biological Sciences & Center for Human Health & the Environment, North Carolina State University, Raleigh, NC 27695, USA
| | - Radhika Dhingra
- Department of Environmental Sciences & Engineering, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
- Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Christina A Markunas
- Behavioral Health Research Division, RTI International, Research Triangle Park, NC 27709, USA
| | - Tao Xu
- Research Unit of Molecular Epidemiology, Helmhotz Zentrum Muenchen, Munich, Germany
| | - Lindsay M Reynolds
- Department of Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Allan C Just
- Department of Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Pooja R Mandaviya
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Brian D Bennett
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Tianyuan Wang
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - The BIOS Consortium
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- Hebrew SeniorLife, Harvard Medical School, Boston, MA 02115, USA
- Framingham Heart Study, Framingham, MA 01702, USA
- Department of Health & Human Services, Division of Extramural Research & Training, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- Department of Pediatric Pulmonology & Pediatric Allergology, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, PO Box 30001, Groningen, The Netherlands
- GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, PO Box 30001, Groningen, The Netherlands
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Center for Genomic Regulation (CRG), Barcelona Institute of Science & Technology, Barcelona, Spain
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
- The Generation R Study Group, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
- Department of Medicine, Epidemiology, & Health Services, Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98101, USA
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Division of Human Nutrition & Health, Wageningen University, Wageningen, The Netherlands
- Epidemiology of Allergic & Respiratory Diseases Department (EPAR), Sorbonne Universités, INSERM, Pierre Louis Institute of Epidemiology & Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
- Centre for Fertility & Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- College of Public Health, University of Kentucky, Lexington, KY 40536, USA
- Department of Biological Sciences & Center for Human Health & the Environment, North Carolina State University, Raleigh, NC 27695, USA
- Department of Environmental Sciences & Engineering, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
- Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, NC 27599, USA
- Behavioral Health Research Division, RTI International, Research Triangle Park, NC 27709, USA
- Research Unit of Molecular Epidemiology, Helmhotz Zentrum Muenchen, Munich, Germany
- Department of Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
- Department of Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Westat, Durham, NC 27703, USA
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York City, NY 10032, USA
- Departments of Obstetrics & Gynecology & Pathology, Duke University School of Medicine, Durham, NC 27708, USA
- Department of Pediatrics, Oslo University Hospital, Oslo, Norway
- National Institute of Public Health, Oslo, Norway
- Centre for Cognitive Ageing & Cognitive Epidemiology, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
- Division of Mental & Physical Health, Norwegian Institute of Public Health, Oslo, Norway
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
- Autonomous Metropolitan University Iztapalapa, Mexico City, Mexico
- Nutrition & Metabolism Section, International Agency for Research on Cancer, Lyon, France
- Center for Research on Population Health, National Institute of Public Health, Mexico
- Hubert Department of Global Health, Emory University, Atlanta, GA 30329, USA
- Institute of Molecular Medicine & Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77225, USA
- Population Sciences Branch, National Heart, Lung, & Blood Institute, National Institutes of Health, Bethesda, MD 01702, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erik Melen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Shanshan Zhao
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | | | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jack A Taylor
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York City, NY 10032, USA
| | - Susan K Murphy
- Departments of Obstetrics & Gynecology & Pathology, Duke University School of Medicine, Durham, NC 27708, USA
| | - Yongmei Liu
- Department of Epidemiology & Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Monica Cheng Munthe-Kaas
- Department of Pediatrics, Oslo University Hospital, Oslo, Norway
- National Institute of Public Health, Oslo, Norway
| | - Ian J Deary
- Centre for Cognitive Ageing & Cognitive Epidemiology, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Wenche Nystad
- Division of Mental & Physical Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmhotz Zentrum Muenchen, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Isabella Annesi-Maesano
- Epidemiology of Allergic & Respiratory Diseases Department (EPAR), Sorbonne Universités, INSERM, Pierre Louis Institute of Epidemiology & Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Karen Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Vincent WV Jaddoe
- The Generation R Study Group, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Donna Arnett
- College of Public Health, University of Kentucky, Lexington, KY 40536, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sharon LR Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
| | - Ken K Ong
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Susan Ewart
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | | | - Isabelle Romieu
- Nutrition & Metabolism Section, International Agency for Research on Cancer, Lyon, France
- Center for Research on Population Health, National Institute of Public Health, Mexico
- Hubert Department of Global Health, Emory University, Atlanta, GA 30329, USA
| | - Nona Sotoodehnia
- Department of Medicine, Epidemiology, & Health Services, Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98101, USA
| | - Myriam Fornage
- Institute of Molecular Medicine & Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77225, USA
| | - Alison Motsinger-Reif
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology & Pediatric Allergology, Beatrix Children’s Hospital, University of Groningen, University Medical Center Groningen, PO Box 30001, Groningen, The Netherlands
- GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, PO Box 30001, Groningen, The Netherlands
| | - Mariona Bustamante
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Center for Genomic Regulation (CRG), Barcelona Institute of Science & Technology, Barcelona, Spain
| | - Daniel Levy
- Framingham Heart Study, Framingham, MA 01702, USA
- Population Sciences Branch, National Heart, Lung, & Blood Institute, National Institutes of Health, Bethesda, MD 01702, USA
| | - Stephanie J London
- Department of Health & Human Services, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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3
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Mahajan A, Taliun D, Thurner M, Robertson NR, Torres JM, Rayner NW, Steinthorsdottir V, Scott RA, Grarup N, Cook JP, Schmidt EM, Wuttke M, Sarnowski C, Mägi R, Nano J, Gieger C, Trompet S, Lecoeur C, Preuss M, Prins BP, Guo X, Bielak LF, Bennett AJ, Bork-Jensen J, Brummett CM, Canouil M, Eckardt KU, Fischer K, Kardia SLR, Kronenberg F, Läll K, Liu CT, Locke AE, Luan J, Ntalla I, Nylander V, Schönherr S, Schurmann C, Yengo L, Bottinger EP, Brandslund I, Christensen C, Dedoussis G, Florez JC, ford I, Franco OH, Frayling TM, Giedraitis V, Hackinger S, Hattersley AT, Herder C, Ikram MA, Ingelsson M, Jørgensen ME, Jørgensen T, Kriebel J, Kuusisto J, Ligthart S, Lindgren CM, Linneberg A, Lyssenko V, Mamakou V, Meitinger T, Mohlke KL, Morris AD, Nadkarni G, Pankow JS, Peters A, Sattar N, Stančáková A, Strauch K, Taylor KD, Thorand B, Thorleifsson G, Thorsteinsdottir U, Tuomilehto J, Witte DR, Dupuis J, Peyser PA, Zeggini E, Loos RJF, Froguel P, Ingelsson E, Lind L, Groop L, Laakso M, Collins FS, Jukema JW, Palmer CNA, Grallert H, Metspalu A, Dehghan A, Köttgen A, Abecasis G, Meigs JB, Rotter JI, Marchini J, Pedersen O, Hansen T, Langenberg C, Wareham NJ, Stefansson K, Gloyn AL, Morris AP, Boehnke M, McCarthy MI. Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps. Nat Genet 2018; 50:1505-1513. [PMID: 30297969 PMCID: PMC6287706 DOI: 10.1038/s41588-018-0241-6] [Citation(s) in RCA: 1019] [Impact Index Per Article: 169.8] [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: 12/26/2017] [Accepted: 08/10/2018] [Indexed: 12/30/2022]
Abstract
We expanded GWAS discovery for type 2 diabetes (T2D) by combining data from 898,130 European-descent individuals (9% cases), after imputation to high-density reference panels. With these data, we (i) extend the inventory of T2D-risk variants (243 loci, 135 newly implicated in T2D predisposition, comprising 403 distinct association signals); (ii) enrich discovery of lower-frequency risk alleles (80 index variants with minor allele frequency <5%, 14 with estimated allelic odds ratio >2); (iii) substantially improve fine-mapping of causal variants (at 51 signals, one variant accounted for >80% posterior probability of association (PPA)); (iv) extend fine-mapping through integration of tissue-specific epigenomic information (islet regulatory annotations extend the number of variants with PPA >80% to 73); (v) highlight validated therapeutic targets (18 genes with associations attributable to coding variants); and (vi) demonstrate enhanced potential for clinical translation (genome-wide chip heritability explains 18% of T2D risk; individuals in the extremes of a T2D polygenic risk score differ more than ninefold in prevalence).
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Affiliation(s)
- Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Daniel Taliun
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Matthias Thurner
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE, UK
| | - Neil R Robertson
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE, UK
| | - Jason M Torres
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - N William Rayner
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE, UK
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | | | - Robert A Scott
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Niels Grarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - James P Cook
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GA, UK
| | - Ellen M Schmidt
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany
| | - Chloé Sarnowski
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, 02118, USA
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Jana Nano
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015CN, The Netherlands
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology 2, Helmholtz Zentrum München, German Research Center for Environmental Health, München-Neuherberg, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Stella Trompet
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, 2300 RC, the Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, 2300 RC, the Netherlands
| | - Cécile Lecoeur
- CNRS-UMR8199, Lille University, Lille Pasteur Institute, Lille, 59000, France
| | - Michael Preuss
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | - Bram Peter Prins
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Xiuqing Guo
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, California, 90502, US
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | | | - Amanda J Bennett
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE, UK
| | - Jette Bork-Jensen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Chad M Brummett
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, MI, 48109, US
| | - Mickaël Canouil
- CNRS-UMR8199, Lille University, Lille Pasteur Institute, Lille, 59000, France
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care Charité, University Medicine Berlin, Berlin, 10117, Germany and German Chronic Kidney Disease study
| | - Krista Fischer
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Sharon LR Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, 6020, Austria and German Chronic Kidney Disease study
| | - Kristi Läll
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
- Institute of Mathematical Statistics, University of Tartu, Tartu, Estonia
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, 02118, USA
| | - Adam E Locke
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Division of Genomics & Bioinformatics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Ioanna Ntalla
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Vibe Nylander
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE, UK
| | - Sebastian Schönherr
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, 6020, Austria and German Chronic Kidney Disease study
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | - Loïc Yengo
- CNRS-UMR8199, Lille University, Lille Pasteur Institute, Lille, 59000, France
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
| | - Ivan Brandslund
- Institute of Regional Health Research, University of Southern Denmark, Odense, 5000, Denmark
- Department of Clinical Biochemistry, Vejle Hospital, Vejle, 7100, Denmark
| | | | - George Dedoussis
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, 17671, Greece
| | - Jose C Florez
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, 02142, USA
| | - Ian ford
- Robertson Centre for Biostatistics, University of Glasgow, Glasgow, UK
| | - Oscar H Franco
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015CN, The Netherlands
| | - Timothy M Frayling
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX1 2LU, UK
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Geriatrics, Uppsala University, Uppsala, SE-751 85, Sweden
| | - Sophie Hackinger
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Andrew T Hattersley
- University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
| | - Christian Herder
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015CN, The Netherlands
| | - Martin Ingelsson
- Department of Public Health and Caring Sciences, Geriatrics, Uppsala University, Uppsala, SE-751 85, Sweden
| | - Marit E Jørgensen
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
- National Institute of Public Health, Southern Denmark University, Copenhagen, 1353, Denmark
| | - Torben Jørgensen
- Research Centre for Prevention and Health, Capital Region of Denmark, Glostrup, 2600, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Medicine, Aalborg University, Aalborg, Denmark
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, 85764, Germany
- German Center for Diabetes Research (DZD), Neuherberg, 85764, Germany
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, 70210, Finland
| | - Symen Ligthart
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015CN, The Netherlands
| | - Cecilia M Lindgren
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, 02142, USA
- Big Data Institute, Li Ka Shing Centre For Health Information and Discovery, University of Oxford, Oxford, OX37BN, UK
| | - Allan Linneberg
- Research Centre for Prevention and Health, Capital Region of Denmark, Glostrup, 2600, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, 20502, Sweden
| | - Vasiliki Mamakou
- Dromokaiteio Psychiatric Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Thomas Meitinger
- Institute of Human Genetics, Technische Universität München, Munich, 81675, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, 27599, USA
| | - Andrew D Morris
- Clinical Research Centre, Centre for Molecular Medicine, Ninewells Hospital and Medical School, Dundee, DD1 9SY, UK
- The Usher Institute to the Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH16 4UX, UK
| | - Girish Nadkarni
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10069, USA
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, 55454, US
| | - Annette Peters
- German Center for Diabetes Research (DZD), Neuherberg, 85764, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, 81675, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Alena Stančáková
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, 70210, Finland
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, 80802, Germany
| | - Kent D Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, California, 90502, US
| | - Barbara Thorand
- German Center for Diabetes Research (DZD), Neuherberg, 85764, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
| | | | - Unnur Thorsteinsdottir
- deCODE Genetics, Amgen inc., Reykjavik, 101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Jaakko Tuomilehto
- Department of Health, National Institute for Health and Welfare, Helsinki, 00271, Finland
- Dasman Diabetes Institute, Dasman, 15462, Kuwait
- Department of Neuroscience and Preventive Medicine, Danube-University Krems, Krems, 3500, Austria
- Diabetes Research Group, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Daniel R Witte
- Department of Public Health, Aarhus University, Aarhus, Denmark
- Danish Diabetes Academy, Odense, Denmark
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, 02118, USA
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, 01702, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Eleftheria Zeggini
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, 10029, USA
- Mindich Child Health and Development Institute, The Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Philippe Froguel
- CNRS-UMR8199, Lille University, Lille Pasteur Institute, Lille, 59000, France
- Department of Genomics of Common Disease, School of Public Health, Imperial College London, London, W12 0NN, UK
| | - Erik Ingelsson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, 94305, US
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, 75185, Sweden
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, SE-751 85, Sweden
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, Malmö, 20502, Sweden
- Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, 70210, Finland
| | - Francis S Collins
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, 2300 RC, the Netherlands
| | - Colin N A Palmer
- Pat Macpherson Centre for Pharmacogenetics and Pharmacogenomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München Research Center for Environmental Health, Neuherberg, 85764, Germany
- German Center for Diabetes Research (DZD), Neuherberg, 85764, Germany
- Clinical Cooparation Group Type 2 Diabetes, Helmholtz Zentrum München, Ludwig-Maximillians University Munich, Germany
- Clinical Cooparation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München, Technical University Munich, Germany
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3015CN, The Netherlands
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, W2 1PG, UK
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, 79106, Germany
| | - Goncalo Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - James B Meigs
- General Medicine Division, Massachusetts General Hospital and Department of Medicine, Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Jerome I Rotter
- Departments of Pediatrics and Medicine, The Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, California, 90502, US
| | - Jonathan Marchini
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Department of Statistics, University of Oxford, Oxford, OX1 3TG, UK
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, 5000, Denmark
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Kari Stefansson
- deCODE Genetics, Amgen inc., Reykjavik, 101, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Anna L Gloyn
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, OX3 7LE, UK
| | - Andrew P Morris
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GA, UK
- Estonian Genome Center, University of Tartu, Tartu, 51010, Estonia
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Mark I McCarthy
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LE, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, OX3 7LE, UK
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4
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Palmer ND, Musani SK, Yerges-Armstrong LM, Feitosa MF, Bielak LF, Hernaez R, Kahali B, Carr JJ, Harris TB, Jhun MA, Kardia SLR, Langefeld CD, Mosley TH, Norris JM, Smith AV, Taylor HA, Wagenknecht LE, Liu J, Borecki IB, Peyser PA, Speliotes EK. Characterization of European ancestry nonalcoholic fatty liver disease-associated variants in individuals of African and Hispanic descent. Hepatology 2013; 58:966-75. [PMID: 23564467 PMCID: PMC3782998 DOI: 10.1002/hep.26440] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 04/03/2013] [Indexed: 12/15/2022]
Abstract
UNLABELLED Nonalcoholic fatty liver disease (NAFLD) is an obesity-related condition affecting over 50% of individuals in some populations and is expected to become the number one cause of liver disease worldwide by 2020. Common, robustly associated genetic variants in/near five genes were identified for hepatic steatosis, a quantifiable component of NAFLD, in European ancestry individuals. Here we tested whether these variants were associated with hepatic steatosis in African- and/or Hispanic-Americans and fine-mapped the observed association signals. We measured hepatic steatosis using computed tomography in five African American (n = 3,124) and one Hispanic American (n = 849) cohorts. All analyses controlled for variation in age, age(2) , gender, alcoholic drinks, and population substructure. Heritability of hepatic steatosis was estimated in three cohorts. Variants in/near PNPLA3, NCAN, LYPLAL1, GCKR, and PPP1R3B were tested for association with hepatic steatosis using a regression framework in each cohort and meta-analyzed. Fine-mapping across African American cohorts was conducted using meta-analysis. African- and Hispanic-American cohorts were 33.9/37.5% male, with average age of 58.6/42.6 years and body mass index of 31.8/28.9 kg/m(2) , respectively. Hepatic steatosis was 0.20-0.34 heritable in African- and Hispanic-American families (P < 0.02 in each cohort). Variants in or near PNPLA3, NCAN, GCKR, PPP1R3B in African Americans and PNPLA3 and PPP1R3B in Hispanic Americans were significantly associated with hepatic steatosis; however, allele frequency and effect size varied across ancestries. Fine-mapping in African Americans highlighted missense variants at PNPLA3 and GCKR and redefined the association region at LYPLAL1. CONCLUSION Multiple genetic variants are associated with hepatic steatosis across ancestries. This explains a substantial proportion of the genetic predisposition in African- and Hispanic-Americans. Missense variants in PNPLA3 and GCKR are likely functional across multiple ancestries.
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Affiliation(s)
- Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC
| | | | | | - Mary F Feitosa
- Department of Genetics, Washington University, St. Louis, MO
| | | | - Ruben Hernaez
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, MD
| | - Bratati Kahali
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - J Jeffrey Carr
- Department of Radiologic Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Tamara B Harris
- National Institute on Aging, National Institutes of Health, Bethesda, MD
| | - Min A Jhun
- Department of Epidemiology, University of Michigan, Ann Arbor, MI
| | - Sharon LR Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI
| | - Carl D Langefeld
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Thomas H Mosley
- Department of Medicine, University of Mississippi, Jackson, MS
| | - Jill M Norris
- Department of Epidemiology, Colorado School of Public Health, Denver, CO
| | | | - Herman A Taylor
- Department of Medicine, University of Mississippi, Jackson, MS
| | - Lynne E Wagenknecht
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Jiankang Liu
- Jackson Heart Study, University of Mississippi, Jackson, MS
| | | | | | - Elizabeth K Speliotes
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
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5
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Stolk L, Perry JRB, Chasman DI, He C, Mangino M, Sulem P, Barbalic M, Broer L, Byrne EM, Ernst F, Esko T, Franceschini N, Gudbjartsson DF, Hottenga JJ, Kraft P, McArdle PF, Porcu E, Shin SY, Smith AV, van Wingerden S, Zhai G, Zhuang WV, Albrecht E, Alizadeh BZ, Aspelund T, Bandinelli S, Lauc LB, Beckmann JS, Boban M, Boerwinkle E, Broekmans FJ, Burri A, Campbell H, Chanock SJ, Chen C, Cornelis MC, Corre T, Coviello AD, d’Adamo P, Davies G, de Faire U, de Geus EJC, Deary IJ, Dedoussis GVZ, Deloukas P, Ebrahim S, Eiriksdottir G, Emilsson V, Eriksson JG, Fauser BCJM, Ferreli L, Ferrucci L, Fischer K, Folsom AR, Garcia ME, Gasparini P, Gieger C, Glazer N, Grobbee DE, Hall P, Haller T, Hankinson SE, Hass M, Hayward C, Heath AC, Hofman A, Ingelsson E, Janssens ACJW, Johnson AD, Karasik D, Kardia SLR, Keyzer J, Kiel DP, Kolcic I, Kutalik Z, Lahti J, Lai S, Laisk T, Laven JSE, Lawlor DA, Liu J, Lopez LM, Louwers YV, Magnusson PKE, Marongiu M, Martin NG, Klaric IM, Masciullo C, McKnight B, Medland SE, Melzer D, Mooser V, Navarro P, Newman AB, Nyholt DR, Onland-Moret NC, Palotie A, Paré G, Parker AN, Pedersen NL, Peeters PHM, Pistis G, Plump AS, Polasek O, Pop VJM, Psaty BM, Räikkönen K, Rehnberg E, Rotter JI, Rudan I, Sala C, Salumets A, Scuteri A, Singleton A, Smith JA, Snieder H, Soranzo N, Stacey SN, Starr JM, Stathopoulou MG, Stirrups K, Stolk RP, Styrkarsdottir U, Sun YV, Tenesa A, Thorand B, Toniolo D, Tryggvadottir L, Tsui K, Ulivi S, van Dam RM, van der Schouw YT, van Gils CH, van Nierop P, Vink JM, Visscher PM, Voorhuis M, Waeber G, Wallaschofski H, Wichmann HE, Widen E, Gent CJMWV, Willemsen G, Wilson JF, Wolffenbuttel BHR, Wright AF, Yerges-Armstrong LM, Zemunik T, Zgaga L, Zillikens MC, Zygmunt M, Arnold AM, Boomsma DI, Buring JE, Crisponi L, Demerath EW, Gudnason V, Harris TB, Hu FB, Hunter DJ, Launer LJ, Metspalu A, Montgomery GW, Oostra BA, Ridker PM, Sanna S, Schlessinger D, Spector TD, Stefansson K, Streeten EA, Thorsteinsdottir U, Uda M, Uitterlinden AG, van Duijn CM, Völzke H, Murray A, Murabito JM, Visser JA, Lunetta KL. Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways. Nat Genet 2012; 44:260-8. [PMID: 22267201 PMCID: PMC3288642 DOI: 10.1038/ng.1051] [Citation(s) in RCA: 246] [Impact Index Per Article: 20.5] [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] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 12/02/2011] [Indexed: 12/13/2022]
Abstract
To newly identify loci for age at natural menopause, we carried out a meta-analysis of 22 genome-wide association studies (GWAS) in 38,968 women of European descent, with replication in up to 14,435 women. In addition to four known loci, we identified 13 loci newly associated with age at natural menopause (at P < 5 × 10(-8)). Candidate genes located at these newly associated loci include genes implicated in DNA repair (EXO1, HELQ, UIMC1, FAM175A, FANCI, TLK1, POLG and PRIM1) and immune function (IL11, NLRP11 and PRRC2A (also known as BAT2)). Gene-set enrichment pathway analyses using the full GWAS data set identified exoDNase, NF-κB signaling and mitochondrial dysfunction as biological processes related to timing of menopause.
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Affiliation(s)
- Lisette Stolk
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Netherlands Consortium of Healthy Aging, Rotterdam, the Netherlands
| | - John RB Perry
- Peninsula Medical School, University of Exeter, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston USA
- Harvard Medical School, Boston, USA
| | - Chunyan He
- Department of Public Health, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, Indiana, USA
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | | | - Maja Barbalic
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Linda Broer
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Enda M Byrne
- Queensland Institute of Medical Research, Brisbane, Australia
| | - Florian Ernst
- Interfakultäres Institut für Genomforschung, Universität Greifswald, Germany
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Estonian Biocenter, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Jouke-Jan Hottenga
- Dept Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, USA
| | - Patick F McArdle
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Eleonora Porcu
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy
| | - So-Youn Shin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Albert V Smith
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Guangju Zhai
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Wei V Zhuang
- Department of Biostatistics, Boston University School of Public Health, Boston Massachusetts, USA
| | - Eva Albrecht
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Behrooz Z Alizadeh
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, the Netherlands
| | - Thor Aspelund
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | | | - Jacques S Beckmann
- Department of Medical Genetics, University of Lausanne, Switzerland
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois (CHUV), University Hospital, Lausanne, Switzerland
| | - Mladen Boban
- Faculty of Medicine, University of Split, Split, Croatia
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Frank J Broekmans
- Department of Reproductive Medicine and Gynaecology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Andrea Burri
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Constance Chen
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Marilyn C Cornelis
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Tanguy Corre
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Andrea D Coviello
- Sections of General Internal Medicine, Preventive Medicine and Epidemiology, Department of Medicine, Boston University School of Medicine, Boston MA, USA
- NHLBI Framingham Heart Study, Framingham, MA, USA
| | - Pio d’Adamo
- Institute for Maternal and Child Health, IRCCS “Burlo Garofolo” Trieste, Italy
- University of Trieste, Trieste, Italy
| | - Gail Davies
- Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Ulf de Faire
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Eco JC de Geus
- Dept Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
- EMGO+ Institute, VU Medical Centre, Amsterdam, The Netherlands
| | - Ian J Deary
- Department of Psychology, The University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, UK
| | | | | | - Shah Ebrahim
- Department of Epidemiology & Population Healths, London School of Hygiene & Tropical Medicine, UK
| | | | | | - Johan G Eriksson
- National Institute for Health and Welfare, Finland
- Department of General Practice and Primary Health Care, University of Helsinki, Finland
- Helsinki University Central Hospital, Unit of General Practice, Helsinki, Finland
- Folkhalsan Research Centre, Helsinki, Finland
- Vasa Central Hospital, Vasa, Finland
| | - Bart CJM Fauser
- Department of Reproductive Medicine and Gynaecology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Liana Ferreli
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy
| | - Luigi Ferrucci
- Longitudinal Studies Section, Clinical Research Branch, National Institute on Aging, Baltimore, Maryland, USA
| | - Krista Fischer
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Aaron R Folsom
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Melissa E Garcia
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, NIH, Bethesda, MD, USA
| | - Paolo Gasparini
- Institute for Maternal and Child Health, IRCCS “Burlo Garofolo” Trieste, Italy
- University of Trieste, Trieste, Italy
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Nicole Glazer
- Sections of General Internal Medicine, Preventive Medicine and Epidemiology, Department of Medicine, Boston University School of Medicine, Boston MA, USA
| | - Diederick E Grobbee
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Toomas Haller
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Susan E Hankinson
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
- Channing Laboratory, Department of Medicine, Brigham and Women.s Hospital Harvard Medical School, Boston, Massachusetts, USA
| | - Merli Hass
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Caroline Hayward
- MRC Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
| | | | - Albert Hofman
- Netherlands Consortium of Healthy Aging, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Erik Ingelsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | | | - David Karasik
- NHLBI Framingham Heart Study, Framingham, MA, USA
- Hebrew SeniorLife Institute for Aging Research and Harvard Medical School, Boston, Massachusetts, USA
| | - Sharon LR Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Jules Keyzer
- Diagnostic GP laboratory Eindhoven, Eindhoven, the Netherlands
| | - Douglas P Kiel
- NHLBI Framingham Heart Study, Framingham, MA, USA
- Hebrew SeniorLife Institute for Aging Research and Harvard Medical School, Boston, Massachusetts, USA
| | - Ivana Kolcic
- Faculty of Medicine, University of Split, Split, Croatia
| | - Zoltán Kutalik
- Department of Medical Genetics, University of Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Switzerland
| | - Jari Lahti
- Institute of Behavioural Sciences, University of Helsinki, Helsinki, Finland
| | - Sandra Lai
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy
| | - Triin Laisk
- Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia
| | - Joop SE Laven
- Division of Reproductive Medicine, Department of Obstetrics & Gynaecology, Erasmus MC, Rotterdam, the Netherlands
| | - Debbie A Lawlor
- MRC Centre for Causal Analysis in Translational Epidemiology, School of Social & Community Medicine, University of Bristol, UK
| | - Jianjun Liu
- Human genetic, Genome Institute of Singapore, Singapore
| | - Lorna M Lopez
- Department of Psychology, The University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, UK
| | - Yvonne V Louwers
- Division of Reproductive Medicine, Department of Obstetrics & Gynaecology, Erasmus MC, Rotterdam, the Netherlands
| | - Patrik KE Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mara Marongiu
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy
| | | | | | - Corrado Masciullo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Sarah E Medland
- Queensland Institute of Medical Research, Brisbane, Australia
| | - David Melzer
- Peninsula Medical School, University of Exeter, UK
| | - Vincent Mooser
- Genetics Division, GlaxoSmithKline, King of Prussia, Pennsylvania, USA
| | - Pau Navarro
- MRC Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Anne B Newman
- Departments of Epidemiology and Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Dale R Nyholt
- Queensland Institute of Medical Research, Brisbane, Australia
| | - N. Charlotte Onland-Moret
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Aarno Palotie
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
- Department of Medical Genetics, University of Helsinki and University Central Hospital, Helsinki, Finland
| | - Guillaume Paré
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston USA
- Harvard Medical School, Boston, USA
- Genetic and Molecular Epidemiology Laboratory, McMaster University, Hamilton, ON Canada
| | - Alex N Parker
- Amgen, Cambridge, MA USA
- Foundation Medicine, Inc., Cambridge MA USA
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Petra HM Peeters
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
| | - Giorgio Pistis
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Andrew S Plump
- Cardiovascular Disease, Merck Research Laboratory, Rahway, NJ, USA
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Split, Croatia
| | - Victor JM Pop
- Department of Clinical Health Psychology, University of Tilburg, Tilburg, the Netherlands
| | - Bruce M Psaty
- Departments of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA USA
- Group Health Research Institute, Group Health Cooperative, Seattle, WA USA
| | - Katri Räikkönen
- Institute of Behavioural Sciences, University of Helsinki, Helsinki, Finland
| | - Emil Rehnberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jerome I Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Igor Rudan
- Faculty of Medicine, University of Split, Split, Croatia
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - Cinzia Sala
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Andres Salumets
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia
| | | | - Andrew Singleton
- Laboratory of Neurogenetics, National Institute of Ageing, Bethesda, MD, USA
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Harold Snieder
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, the Netherlands
- LifeLines Cohort Study & Biobank, University Medical Center Groningen, University of Groningen, the Netherlands
| | - Nicole Soranzo
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, UK
- Geriatric Medicine Unit, University of Edinburgh, Edinburgh, UK
| | - Maria G Stathopoulou
- Department of Nutrition and Dietetics, Harokopio University, Athens, Greece
- Cardiovascular Genetics Research Unit, EA4373, Université Henri Poincaré - Nancy 1, Nancy, France
| | - Kathleen Stirrups
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Ronald P Stolk
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, the Netherlands
- LifeLines Cohort Study & Biobank, University Medical Center Groningen, University of Groningen, the Netherlands
| | | | - Yan V Sun
- Department of Epidemiology, Emory University, Atlanta, GA, USA
| | - Albert Tenesa
- MRC Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, UK
| | - Barbara Thorand
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Daniela Toniolo
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
- Institute of Molecular Genetics-CNR, Pavia, Italy
| | - Laufey Tryggvadottir
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Icelandic Cancer Registry, Reykjavik, Iceland
| | | | - Sheila Ulivi
- Institute for Maternal and Child Health, IRCCS “Burlo Garofolo” Trieste, Italy
| | - Rob M van Dam
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
- Saw Swee Hock School of Public Health and Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yvonne T van der Schouw
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Carla H van Gils
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Peter van Nierop
- Municipal Health Service Brabant-Zuidoost, Helmond, the Netherlands
| | - Jacqueline M Vink
- Dept Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Peter M Visscher
- Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, UK
- Genetic Epidemiology, Queensland Institute of Medical Research, Brisbane, Australia
| | - Marlies Voorhuis
- Department of Reproductive Medicine and Gynaecology, University Medical Center Utrecht, Utrecht, the Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gérard Waeber
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois (CHUV), University Hospital, Lausanne, Switzerland
| | - Henri Wallaschofski
- Institute for Clinical Chemistry and Laboratory Medicine, University of Greifswald
| | - H Erich Wichmann
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
- Klinikum Grosshadern, Munich, Germany
| | - Elisabeth Widen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
| | | | - Gonneke Willemsen
- Dept Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - James F Wilson
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
| | - Bruce HR Wolffenbuttel
- LifeLines Cohort Study & Biobank, University Medical Center Groningen, University of Groningen, the Netherlands
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, the Netherlands
| | - Alan F Wright
- MRC Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Laura M Yerges-Armstrong
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - Lina Zgaga
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK
- Andrija Stampar School of Public Health, Medical School, University of Zagreb, Zagreb, Croatia
| | | | - Marek Zygmunt
- Klinik für Gynäkologie und Geburtshilfe, Universität Greifswald, Germany
| | - The LifeLines Cohort Study
- LifeLines Cohort Study & Biobank, University Medical Center Groningen, University of Groningen, the Netherlands
| | - Alice M Arnold
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Dorret I Boomsma
- Dept Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
- EMGO+ Institute, VU Medical Centre, Amsterdam, The Netherlands
| | - Julie E. Buring
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston USA
- Harvard Medical School, Boston, USA
- Harvard School of Public Health, Boston, MA USA
| | - Laura Crisponi
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy
| | - Ellen W Demerath
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Tamara B Harris
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, NIH, Bethesda, MD, USA
| | - Frank B Hu
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
- Channing Laboratory, Department of Medicine, Brigham and Women.s Hospital Harvard Medical School, Boston, Massachusetts, USA
| | - David J Hunter
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, USA
- Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
- Channing Laboratory, Department of Medicine, Brigham and Women.s Hospital Harvard Medical School, Boston, Massachusetts, USA
| | - Lenore J Launer
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, NIH, Bethesda, MD, USA
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Estonian Biocenter, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia
| | | | - Ben A Oostra
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston USA
- Harvard Medical School, Boston, USA
- Harvard School of Public Health, Boston, MA USA
- Division of Cardiology, Brigham and Women’s Hospital, Boston, MA USA
| | - Serena Sanna
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy
| | - David Schlessinger
- National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
| | - Kari Stefansson
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Elizabeth A Streeten
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Manuela Uda
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Netherlands Consortium of Healthy Aging, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Henry Völzke
- Institut für Community Medicine, Universität Greifswald, Germany
| | - Anna Murray
- Peninsula Medical School, University of Exeter, UK
| | - Joanne M Murabito
- Sections of General Internal Medicine, Preventive Medicine and Epidemiology, Department of Medicine, Boston University School of Medicine, Boston MA, USA
- NHLBI Framingham Heart Study, Framingham, MA, USA
| | - Jenny A Visser
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston Massachusetts, USA
- NHLBI Framingham Heart Study, Framingham, MA, USA
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Lai MM, Li CI, Kardia SLR, Liu CS, Lin WY, Lee YD, Chang PC, Lin CC, Li TC. Sex difference in the association of metabolic syndrome with high sensitivity C-reactive protein in a Taiwanese population. BMC Public Health 2010; 10:429. [PMID: 20663138 PMCID: PMC2920887 DOI: 10.1186/1471-2458-10-429] [Citation(s) in RCA: 24] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 07/21/2010] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Although sex differences have been reported for associations between components of metabolic syndrome and inflammation, the question of whether there is an effect modification by sex in the association between inflammation and metabolic syndrome has not been investigated in detail. Therefore, the aim of this study was to compare associations of high sensitivity C-creative protein (hs-CRP) with metabolic syndrome and its components between men and women. METHODS A total of 1,305 subjects aged 40 years and over were recruited in 2004 in a metropolitan city in Taiwan. The biochemical indices, such as hs-CRP, fasting glucose levels, lipid profiles, urinary albumin, urinary creatinine and anthropometric indices, were measured. Metabolic syndrome was defined using the American Heart Association and the National Heart, lung and Blood Institute (AHA/NHLBI) definition. The relationship between metabolic syndrome and hs-CRP was examined using multivariate logistic regression analysis. RESULTS After adjustment for age and lifestyle factors including smoking, and alcohol intake, elevated concentrations of hs-CRP showed a stronger association with metabolic syndrome in women (odds ratio comparing tertile extremes 4.80 [95% CI: 3.31-6.97]) than in men (2.30 [1.65-3.21]). The p value for the sex interaction was 0.002. All components were more strongly associated with metabolic syndrome in women than in men, and all sex interactions were significant except for hypertension. CONCLUSIONS Our data suggest that inflammatory processes may be of particular importance in the pathogenesis of metabolic syndrome in women.
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Affiliation(s)
- Ming-May Lai
- Department of Family Medicine, China Medical University & Hospital, Taichung, Taiwan
- Department of Family Medicine, College of Medicine, China Medical University & Hospital, Taichung, Taiwan
| | - Chia-Ing Li
- Medical Research, China Medical University & Hospital, Taichung, Taiwan
| | - Sharon LR Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan
| | - Chiu-Shong Liu
- Department of Family Medicine, China Medical University & Hospital, Taichung, Taiwan
- Department of Family Medicine, College of Medicine, China Medical University & Hospital, Taichung, Taiwan
| | - Wen-Yuan Lin
- Department of Family Medicine, China Medical University & Hospital, Taichung, Taiwan
- Department of Family Medicine, College of Medicine, China Medical University & Hospital, Taichung, Taiwan
| | - Yih-Dar Lee
- Department of Psychiatric, Medical College, National Cheng-Kung University, Tainan, Taiwan
- Bristol-Myers Squibb (Taiwan) Ltd, Global Development & Medical Affair, Tainan, Taiwan
| | - Pei-Chia Chang
- Administration Center, China Medical University & Hospital, Taichung, Taiwan
| | - Cheng-Chieh Lin
- Department of Family Medicine, China Medical University & Hospital, Taichung, Taiwan
- Department of Family Medicine, College of Medicine, China Medical University & Hospital, Taichung, Taiwan
- Institute of Health Care Administration, College of Health Science, Asia University, Taichung, Taiwan
- School and Graduate Institute of Health Care Administration, College of Public Health, China Medical University & Hospital, Taichung, Taiwan
| | - Tsai-Chung Li
- Institute of Health Care Administration, College of Health Science, Asia University, Taichung, Taiwan
- Graduate Institute of Biostatistics & Chinese Medicine Science, China Medical University & Hospital, Taichung, Taiwan
- Biostatistics Center, China Medical University & Hospital, Taichung, Taiwan
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Smith JA, Turner ST, Sun YV, Fornage M, Kelly RJ, Mosley TH, Jack CR, Kullo IJ, Kardia SLR. Complexity in the genetic architecture of leukoaraiosis in hypertensive sibships from the GENOA Study. BMC Med Genomics 2009; 2:16. [PMID: 19351393 PMCID: PMC2679055 DOI: 10.1186/1755-8794-2-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Accepted: 04/07/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Subcortical white matter hyperintensity on magnetic resonance imaging (MRI) of the brain, referred to as leukoaraiosis, is associated with increased risk of stroke and dementia. Hypertension may contribute to leukoaraiosis by accelerating the process of arteriosclerosis involving penetrating small arteries and arterioles in the brain. Leukoaraiosis volume is highly heritable but shows significant inter-individual variability that is not predicted well by any clinical covariates (except for age) or by single SNPs. METHODS As part of the Genetics of Microangiopathic Brain Injury (GMBI) Study, 777 individuals (74% hypertensive) underwent brain MRI and were genotyped for 1649 SNPs from genes known or hypothesized to be involved in arteriosclerosis and related pathways. We examined SNP main effects, epistatic (gene-gene) interactions, and context-dependent (gene-environment) interactions between these SNPs and covariates (including conventional and novel risk factors for arteriosclerosis) for association with leukoaraiosis volume. Three methods were used to reduce the chance of false positive associations: 1) false discovery rate (FDR) adjustment for multiple testing, 2) an internal replication design, and 3) a ten-iteration four-fold cross-validation scheme. RESULTS Four SNP main effects (in F3, KITLG, CAPN10, and MMP2), 12 SNP-covariate interactions (including interactions between KITLG and homocysteine, and between TGFB3 and both physical activity and C-reactive protein), and 173 SNP-SNP interactions were significant, replicated, and cross-validated. While a model containing the top single SNPs with main effects predicted only 3.72% of variation in leukoaraiosis in independent test samples, a multiple variable model that included the four most highly predictive SNP-SNP and SNP-covariate interactions predicted 11.83%. CONCLUSION These results indicate that the genetic architecture of leukoaraiosis is complex, yet predictive, when the contributions of SNP main effects are considered in combination with effects of SNP interactions with other genes and covariates.
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Affiliation(s)
- Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Stephen T Turner
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic and Foundation, Rochester, MN, USA
| | - Yan V Sun
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Myriam Fornage
- Human Genetics Center and Institute of Molecular Medicine, University of Texas-Houston Health Science Center, Houston, TX, USA
| | - Reagan J Kelly
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Thomas H Mosley
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Clifford R Jack
- Department of Diagnostic Radiology, Mayo Clinic and Foundation, Rochester, MN, USA
| | - Iftikhar J Kullo
- Division of Cardiovascular Diseases, Department of Internal Medicine, Mayo Clinic and Foundation, Rochester, MN, USA
| | - Sharon LR Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
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Kardia SLR, Sun YV, Hamon SC, Barkley RA, Boerwinkle E, Turner ST. Interactions between the adducin 2 gene and antihypertensive drug therapies in determining blood pressure in people with hypertension. BMC Med Genet 2007; 8:61. [PMID: 17854487 PMCID: PMC2065870 DOI: 10.1186/1471-2350-8-61] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2007] [Accepted: 09/13/2007] [Indexed: 01/09/2023]
Abstract
BACKGROUND As part of the NHLBI Family Blood Pressure Program, the Genetic Epidemiology Network of Arteriopathy (GENOA) recruited 575 sibships (n = 1583 individuals) from Rochester, MN who had at least two hypertensive siblings diagnosed before age 60. Linkage analysis identified a region on chromosome 2 that was investigated using 70 single nucleotide polymorphisms (SNPs) typed in 7 positional candidate genes, including adducin 2 (ADD2). METHOD To investigate whether blood pressure (BP) levels in these hypertensives (n = 1133) were influenced by gene-by-drug interactions, we used cross-validation statistical methods (i.e., estimating a model for predicting BP levels in one subgroup and testing it in a different subgroup). These methods greatly reduced the chance of false positive findings. RESULTS Eight SNPs in ADD2 were significantly associated with systolic BP in untreated hypertensives (p-value < 0.05). Moreover, we also identified SNPs associated with gene-by-drug interactions on systolic BP in drug-treated hypertensives. The TT genotype at SNP rs1541582 was associated with an average systolic BP of 133 mmHg in the beta-blocker subgroup and 148 mmHg in the diuretic subgroup after adjusting for overall mean differences among drug classes. CONCLUSION Our findings suggest that hypertension candidate gene variation may influence BP responses to specific antihypertensive drug therapies and measurement of genetic variation may assist in identifying subgroups of hypertensive patients who will benefit most from particular antihypertensive drug therapies.
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Affiliation(s)
- Sharon LR Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Yan V Sun
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Sara C Hamon
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Ruth Ann Barkley
- Human Genetics Center, University of Texas Health Sciences Center, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Sciences Center, Houston, TX, USA
| | - Stephen T Turner
- Department of Internal Medicine and Division of Hypertension, Mayo Clinic, Rochester, MN, USA
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Kardia SLR, Bodzin J, Goldenberg A, Citrin T, Raup SF, Bach JV. Genomics and public health: development of Web-based training tools for increasing genomic awareness. Prev Chronic Dis 2005; 2:A25. [PMID: 15888236 PMCID: PMC1327719] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In 2001, the Centers for Disease Control and Prevention funded three Centers for Genomics and Public Health to develop training tools for increasing genomic awareness. Over the past three years, the centers, working together with the Centers for Disease Control and Prevention's Office of Genomics and Disease Prevention, have developed tools to increase awareness of the impact genomics will have on public health practice, to provide a foundation for understanding basic genomic advances, and to translate the relevance of that information to public health practitioners' own work. These training tools serve to communicate genomic advances and their potential for integration into public heath practice. This paper highlights two of these training tools: 1) Genomics for Public Health Practitioners: The Practical Application of Genomics in Public Health Practice, a Web-based introduction to genomics, and 2) Six Weeks to Genomic Awareness, an in-depth training module on public health genomics. This paper focuses on the processes and collaborative efforts by which these live presentations were developed and delivered as Web-based training sessions.
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Affiliation(s)
- Sharon LR Kardia
- Michigan Center for Genomics & Public Health, University of Michigan, School of Public Health, Department of Epidemiology
| | - Jennifer Bodzin
- Michigan Center for Genomics & Public Health, University of Michigan, School of Public Health, Ann Arbor, Mich
| | - Aaron Goldenberg
- Michigan Center for Genomics & Public Health, University of Michigan, School of Public Health, Ann Arbor, Mich
| | - Toby Citrin
- Michigan Center for Genomics & Public Health, University of Michigan, School of Public Health, Ann Arbor, Mich
| | - Sarah F Raup
- Center for Genomics & Public Health, University of Washington, Seattle, Wash
| | - Janice V Bach
- Michigan Department of Community Health, Epidemiology Services Division, Genomics Program, Lansing, Mich
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Margulies EH, Kardia SL, Innis JW. A comparative molecular analysis of developing mouse forelimbs and hindlimbs using serial analysis of gene expression (SAGE). Genome Res 2001; 11:1686-98. [PMID: 11591645 PMCID: PMC311149 DOI: 10.1101/gr.192601] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [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: 11/25/2022]
Abstract
The analysis of differentially expressed genes is a powerful approach to elucidate the genetic mechanisms underlying the morphological and evolutionary diversity among serially homologous structures, both within the same organism (e.g., hand vs. foot) and between different species (e.g., hand vs. wing). In the developing embryo, limb-specific expression of Pitx1, Tbx4, and Tbx5 regulates the determination of limb identity. However, numerous lines of evidence, including the fact that these three genes encode transcription factors, indicate that additional genes are involved in the Pitx1-Tbx hierarchy. To examine the molecular distinctions coded for by these factors, and to identify novel genes involved in the determination of limb identity, we have used Serial Analysis of Gene Expression (SAGE) to generate comprehensive gene expression profiles from intact, developing mouse forelimbs and hindlimbs. To minimize the extraction of erroneous SAGE tags from low-quality sequence data, we used a new algorithm to extract tags from -analyzed sequence data and obtained 68,406 and 68,450 SAGE tags from forelimb and hindlimb SAGE libraries, respectively. We also developed an improved method for determining the identity of SAGE tags that increases the specificity of and provides additional information about the confidence of the tag-UniGene cluster match. The most differentially expressed gene between our SAGE libraries was Pitx1. The differential expression of Tbx4, Tbx5, and several limb-specific Hox genes was also detected; however, their abundances in the SAGE libraries were low. Because numerous other tags were differentially expressed at this low level, we performed a 'virtual' subtraction with 362,344 tags from six additional nonlimb SAGE libraries to further refine this set of candidate genes. This subtraction reduced the number of candidate genes by 74%, yet preserved the previously identified regulators of limb identity. This study presents the gene expression complexity of the developing limb and identifies candidate genes involved in the regulation of limb identity. We propose that our computational tools and the overall strategy used here are broadly applicable to other SAGE-based studies in a variety of organisms. [SAGE data are all available at GEO (http://www.ncbi.nlm.nih.gov/geo/) under accession nos. GSM55 and GSM56, which correspond to the forelimb and hindlimb raw SAGE data.]
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Affiliation(s)
- E H Margulies
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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Abstract
Serial Analysis of Gene Expression (SAGE) is becoming a widely used gene expression profiling method for the study of development, cancer and other human diseases. Investigators using SAGE rely heavily on the quantitative aspect of this method for cataloging gene expression and comparing multiple SAGE libraries. We have developed additional computational and statistical tools to assess the quality and reproducibility of a SAGE library. Using these methods, a critical variable in the SAGE protocol was identified that has the potential to bias the Tag distribution relative to the GC content of the 10 bp SAGE Tag DNA sequence. We also detected this bias in a number of publicly available SAGE libraries. It is important to note that the GC content bias went undetected by quality control procedures in the current SAGE protocol and was only identified with the use of these statistical analyses on as few as 750 SAGE Tags. In addition to keeping any solution of free DiTags on ice, an analysis of the GC content should be performed before sequencing large numbers of SAGE Tags to be confident that SAGE libraries are free from experimental bias.
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Affiliation(s)
- E H Margulies
- Department of Human Genetics, University of Michigan Medical School and Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
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Klos KL, Kardia SL, Ferrell RE, Turner ST, Boerwinkle E, Sing CF. Genome-wide linkage analysis reveals evidence of multiple regions that influence variation in plasma lipid and apolipoprotein levels associated with risk of coronary heart disease. Arterioscler Thromb Vasc Biol 2001; 21:971-8. [PMID: 11397706 DOI: 10.1161/01.atv.21.6.971] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [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: 11/16/2022]
Abstract
Results of genome-wide linkage analyses to identify chromosomal regions that influence interindividual variation in plasma lipid and apolipoprotein levels in the Rochester, Minn, population are reported. Analyses were conducted for total cholesterol (total-C), triglycerides (TGs), high density lipoprotein cholesterol (HDL-C), apolipoprotein A-I, apolipoprotein A-II, apolipoprotein B, apolipoprotein C-II, apolipoprotein C-III, apolipoprotein E, the total-C/HDL-C ratio, and the TG/HDL-C ratio. Genotypes were measured for 373 genome-wide marker loci on 1484 individuals distributed among 232 multigeneration pedigrees sampled without regard to health status. LOD scores and estimates of additive genetic variance associated with map locations were obtained by using the variance-component method of linkage analysis. No evidence of linkage with genes influencing variation in age served as a negative control. Plasma apolipoprotein E levels and the apolipoprotein E gene served as a positive control (LOD score 4.20). Evidence (LOD score >2.00) was provided that was suggestive of a gene or genes on chromosomes 4 and 5 influencing variation in the apolipoprotein A-II level, on chromosome 12 influencing variation in the apolipoprotein A-I level, and on chromosome 17 influencing variation of total-C/HDL-C. These analyses provide new information about genomic regions in humans that influence interindividual variation in plasma lipid and apolipoprotein levels and serve as a basis for further fine-mapping studies to identify new genes involved in lipid metabolism.
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Affiliation(s)
- K L Klos
- Department of Human Genetics, University of Michigan, Ann Arbor 48109-0618, USA
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13
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Nelson MR, Kardia SL, Ferrell RE, Sing CF. A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation. Genome Res 2001; 11:458-70. [PMID: 11230170 PMCID: PMC311041 DOI: 10.1101/gr.172901] [Citation(s) in RCA: 298] [Impact Index Per Article: 13.0] [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: 11/27/2000] [Accepted: 01/02/2001] [Indexed: 11/24/2022]
Abstract
Recent advances in genome research have accelerated the process of locating candidate genes and the variable sites within them and have simplified the task of genotype measurement. The development of statistical and computational strategies to utilize information on hundreds -- soon thousands -- of variable loci to investigate the relationships between genome variation and phenotypic variation has not kept pace, particularly for quantitative traits that do not follow simple Mendelian patterns of inheritance. We present here the combinatorial partitioning method (CPM) that examines multiple genes, each containing multiple variable loci, to identify partitions of multilocus genotypes that predict interindividual variation in quantitative trait levels. We illustrate this method with an application to plasma triglyceride levels collected on 188 males, ages 20--60 yr, ascertained without regard to health status, from Rochester, Minnesota. Genotype information included measurements at 18 diallelic loci in six coronary heart disease--candidate susceptibility gene regions: APOA1--C3--A4, APOB, APOE, LDLR, LPL, and PON1. To illustrate the CPM, we evaluated all possible partitions of two-locus genotypes into two to nine partitions (approximately 10(6) evaluations). We found that many combinations of loci are involved in sets of genotypic partitions that predict triglyceride variability and that the most predictive sets show nonadditivity. These results suggest that traditional methods of building multilocus models that rely on statistically significant marginal, single-locus effects, may fail to identify combinations of loci that best predict trait variability. The CPM offers a strategy for exploring the high-dimensional genotype state space so as to predict the quantitative trait variation in the population at large that does not require the conditioning of the analysis on a prespecified genetic model.
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Affiliation(s)
- M R Nelson
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109-0618, USA
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Kelada SN, Kardia SL, Walker AH, Wein AJ, Malkowicz SB, Rebbeck TR. The glutathione S-transferase-mu and -theta genotypes in the etiology of prostate cancer: genotype-environment interactions with smoking. Cancer Epidemiol Biomarkers Prev 2000; 9:1329-34. [PMID: 11142418] [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: 02/18/2023] Open
Abstract
It has been reported that individuals who express GSTT1, the gene coding for the theta class of the glutathione S-transferases (GSTs), have an elevated risk of prostate cancer (CaP). This result is supported by studies that show glutathione conjugation of some xenobiotics by the GSTs can produce mutagenic intermediates. However, the potential role of environmental factors in modifying the risk of CaP conferred by GSTT1 is not known. We investigated whether there was an interaction between smoking and the non-deleted genotypes of the mu (GSTM1) and theta (GSTT1) GST genes using a clinic-based study of 276 CaP cases and 499 controls. We observed no main effect of smoking (odds ratio, 0.95; confidence interval, 0.69-1.29) or GSTM1 (odds ratio, 1.00; confidence interval, 0.73-1.36) with CaP, but did observe a statistically significant main effect of GSTT1 with CaP (odds ratio, 1.61; confidence interval, 1.14-2.28) as reported previously. No interaction between smoking and GSTM1 was observed. A significant increase in the probability of having CaP was observed in men who were both smokers and carried a non-deleted GSTT1 genotype compared with men who had neither or only one of these risk factors (P = 0.049). Approximately 30.9% of CaP cases in this study could be attributed to the smoking x GSTT1 interaction. Whereas the mechanism of this interaction is not known, it is plausible that the metabolism of carcinogenic intermediates or the response to chronic inflammation associated with smoking may be modulated by the GSTT1 genotype and may modify CaP risk.
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Affiliation(s)
- S N Kelada
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor 48109, USA
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Abstract
The term syndrome X has been applied to the association of hypertension, non-insulin-dependent diabetes mellitus (NIDDM), android obesity, insulin resistance, and dyslipidemia. In this paper, based on population samples from Tecumseh, Michigan, and Hiroshima, Japan, characterized by persons > or = 40 years of age, we examine the validity of regarding this constellation of traits as a true syndrome, i.e., an array of traits with a single, unifying pathophysiology underlying its components. Data were not available on insulin resistance and dyslipidemia, and obesity was expressed as body mass index (BMI) without the division into android and non-android types. The four ethnic-gender data sets were analyzed on the basis of two age classes, age > or = 40 years and age > or = 50 years, and two obesity classes, BMI > or = 27 and > or = 30. A simple chi 2 test of goodness-of-fit under a model of independence revealed non-random associations between hypertension, NIDDM, and BMI which were in part attributable to an excess of persons with all three traits. However, when the four data sets were subjected to separate log-linear analyses of the three-way association tables, none of the three-factor interaction terms (i.e., syndrome X) was significant. High significance was, however, observed in the two-factor interaction term for BMI*hypertension. It is concluded that the significant association between these three traits is driven by the BMI*hypertension interaction, and there is no evidence in these data sets of a significant role for a syndrome X. Genet.
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Affiliation(s)
- J V Neel
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, USA
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Abstract
In Milan hypertensive rats, a variant in the alpha-adducin gene has been shown to account for approximately 50% of the interindividual variation in blood pressure levels between these animals and their normotensive counterparts. Additional studies have suggested that a polymorphism within exon 10 of the human alpha-adducin gene (Gly-460-Trp) may be associated with hypertension and salt sensitivity. On the basis of these observations, we investigated variation within or near the human alpha-adducin gene for linkage and association with a locus influencing blood pressure levels in 281 nuclear families (774 siblings aged 5 to 37 years; 380 parents aged 26 to 57 years), selected from the white population of Rochester, Minnesota, without regard to health. Sib pair linkage analyses (n = 852 sibling pairs) using a dinucleotide repeat marker (D4S43) that maps approximately 660 kb from the alpha-adducin gene provided no evidence of linkage between this marker locus and a locus influencing systolic, diastolic, or mean blood pressure levels. Allele frequencies for the Gly-460-Trp polymorphism were similar to those reported in other white populations (Gly = 0.812, Trp = 0.188); however, this polymorphism was not associated with any measure of blood pressure level in either parents or siblings. Therefore, variation within the alpha-adducin gene does not appear to have a major influence on measures of blood pressure in white families from Rochester, Minnesota.
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Affiliation(s)
- M S Bray
- Institute for Molecular Medicine, University of Texas-Houston Health Science Center, 77225, USA
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17
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Abstract
There is a growing frustration with the limitations and inconsistencies of single locus candidate gene association and linkage studies. This frustration is exacerbated by the knowledge that a large influx of genotypic and gene expression data is expected to emerge over the next 5 years, and we are not prepared for the type of multigenic conceptual framework that will be necessary to analyze that data. A review of the hypertension genetic literature reveals substantial evidence for the importance of both genetic and environmental contexts on the mapping between single locus polymorphisms and risk of disease. These trends indicate that the current reliance on simple single gene studies to elucidate the complex etiology of hypertension needs to undergo some kind of transformation. It is suggested that even a minor shift to a more systematic investigation of context-dependent effects will increase our understanding of the multidimensional genetic and environmental realities underneath current studies. This shift is also necessary if we are to gain a deeper understanding of the specific ways in which an individual's risk of hypertension is a consequence of the inter- actions among genes and environments.
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Affiliation(s)
- S L Kardia
- Department of Epidemiology, University of Michigan, 109 Observatory Street, Ann Arbor, MI 48109-2029, USA
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18
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Stengård JH, Kardia SL, Tervahauta M, Ehnholm C, Nissinen A, Sing CF. Utility of the predictors of coronary heart disease mortality in a longitudinal study of elderly Finnish men aged 65 to 84 years is dependent on context defined by Apo E genotype and area of residence. Clin Genet 1999; 56:367-77. [PMID: 10668927 DOI: 10.1034/j.1399-0004.1999.560505.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [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: 11/23/2022]
Abstract
A common assumption underlying most genetic studies is that individuals with different genotypes respond similarly to exposure to internal (epigenetic and background genotype effects) and external (ecological) environments. Here we evaluate whether this assumption is true in individuals with different genotypes of the gene coding for the apolipoprotein E (Apo E) molecule, an important determinant of the metabolic fate of plasma lipids and lipoproteins. We addressed whether the utility of known risk factors of coronary heart disease (CHD) in the prediction of CHD death in a 5-year follow-up is the same for the two most common Apo E genotypes, epsilon3/3 and epsilon4/3, in two cohorts of elderly Finnish men (age at baseline: 65-84 years), one in Eastern and the other in Southwestern Finland. The CHD mortality rate was higher in the epsilon4/3 than in the epsilon3/3 genotype in both cohorts (11.1 versus 7.8%, Pr = 0.281 in the Eastern cohort and 19.6 versus 8.2%, Pr = 0.002 in the Southwestern cohort). In the Eastern cohort, serum high density lipoprotein (HDL) cholesterol level was identified as a strong predictor of CHD death in the epsilon3/3 genotype (beta = -2.155, Pr = 0.019). In the Southwestern cohort, age (beta = 0.139, Pr = 0.006), body mass index (BMI) (beta = 0.149, Pr = 0.016), and serum total cholesterol level (beta = 0.453, Pr = 0.051) were identified as strong predictors in the epsilon3/3 genotype, as were smoking (beta = 0.236, Pr = 0.008) and BMI (beta = -0.124, Pr = 0.057) in the epsilon4/3 genotype. The latter observation indicates that in Southwestern Finland the probability of CHD death decreases with increasing BMI in elderly men with the epsilon4/3 genotype, while in their counterparts with the epsilon3/3 genotype the risk increases with increasing BMI. This difference was statistically significant (Pr = 0.002). These observations clearly argue against the assumption that individuals with different genotypes respond similarly to exposures to internal and/or external environments. These observations are consistent with a complex pathobiology of CHD involving biochemical and physiological agents that are under the influence of interactions between genetic and environmental factors. Information about these interactions is necessary for developing a more precise risk assessment and ultimately to improve public health and clinical strategies to prevent this devastating disease both at the individual and population levels.
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Affiliation(s)
- J H Stengård
- National Public Health Institute, Helsinki, Finland.
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Nelson MR, Kardia SL, Ferrell RE, Sing CF. Influence of apolipoprotein E genotype variation on the means, variances, and correlations of plasma lipids and apolipoproteins in children. Ann Hum Genet 1999; 63:311-28. [PMID: 10738543 DOI: 10.1046/j.1469-1809.1999.6340311.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [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: 11/20/2022]
Abstract
The impact of the three most common apolipoprotein E (APOE) genotypes (epsilon 32, epsilson 33, and epsilon 43) on means, variances, and correlations of nine plasma lipid and apolipoprotein traits (total cholesterol, InTriglycerides, HDL cholesterol, and apolipoproteins AI, AII, B, CII, CIII, and InE) was studied in 212 unrelated female and 219 unrelated male children aged 5-21.5 years from 278 pedigrees ascertained without regard to health status from Rochester, Minnesota. There was significant heterogeneity (p < or = 0.05) among genotypes for the mean plasma levels of InApo E, Apo CII, Apo CIII, and InTriglycerides (InTrig) in females, and for the means of InApo E, Apo B, and total cholesterol (Total-C) in males. Significant heterogeneity of intragenotypic variance was observed in males for Apo CII, InTrig, and HDL-C; no significant heterogeneity was observed in females. Pairwise correlations between traits differed significantly among APOE genotypes in both females (6 of 36 pairs) and males (5 of 36 pairs). These results differ from those obtained from studies of the parental generation from the same sample of pedigrees. Our study further demonstrates that, with the exception of mean InApo E levels, the univariate and bivariate distributions of traits that are measures of lipoprotein metabolism are influenced by variation in the APOE gene in a gender- and generation-dependent manner.
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Affiliation(s)
- M R Nelson
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor 48109-0618, USA
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Kardia SL, Haviland MB, Ferrell RE, Sing CF. The relationship between risk factor levels and presence of coronary artery calcification is dependent on apolipoprotein E genotype. Arterioscler Thromb Vasc Biol 1999; 19:427-35. [PMID: 9974428 DOI: 10.1161/01.atv.19.2.427] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [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: 11/16/2022]
Abstract
An important research question in the study of the genetics of coronary artery disease (CAD) is whether information about genetic variation will improve our ability to predict CAD beyond established risk factors. This question is especially relevant to the goal of identifying young, asymptomatic adults with coronary atherosclerosis who would benefit most from interventions to reduce risk. Coronary artery calcification (CAC) detected by electron-beam computed tomography is a relatively new method for detecting coronary atherosclerosis in asymptomatic individuals that has been shown to be a more accurate indicator of coronary atherosclerosis in asymptomatic individuals than other noninvasive techniques. In a study of asymptomatic women (n=169) and men (n=160) between the ages of 20 and 59 representative of the Rochester, Minnesota population, we used logistic regression to ask whether the most common Apolipoprotein (Apo) E genotypes (epsilon3/2, epsilon3/3, and epsilon4/3) predict the presence of CAC. The addition of information about ApoE genotypes to logistic models containing each separate risk factor did not improve prediction of CAC (P>0.10 in both women and men). However, there was significant evidence (P<0.10) that associations between variation in the probability of having CAC and variation in body mass index, plasma total cholesterol, and plasma ApoB in men and body mass index, plasma triglycerides, plasma ApoA1, and plasma ApoE in women were dependent on ApoE genotype. Thus, variation in the gene coding for ApoE may play a role in determining the contribution of established risk factors to risk of CAC.
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Affiliation(s)
- S L Kardia
- Department of Human Genetics, University of Michigan, Ann Arbor 48109- 0618, USA.
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Affiliation(s)
- O F Pomerleau
- Department of Psychiatry, School of Medicine, University of Michigan, Ann Arbor 48108, USA.
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Abstract
The atherosclerotic process begins in childhood but, in general, does not reach the clinical horizon until after the fifth decade of life, at which point the best opportunities for prevention and intervention have been lost. In order to identify children with a high risk of developing coronary artery disease (CAD), risk factors measured in children that are the most informative indicators of future risk must be identified. Using a novel analytical strategy that incorporates a continuum of information about context dependency, we investigated whether there were significant differences in intermediate biochemical and physiological traits between children (189 females and 188 males, ages 5-20.5 years) with and without a strong family history of clinically-defined CAD at three levels of context dependency (coarse grain, medium grain, and fine grain). In the coarse-grained analysis we tested for differences in mean levels of nine intermediate traits (lipids, apolipoproteins, blood pressure traits) and indices of external and internal environmental context (age, body mass index, smoking status). Female children with a strong family history had higher average levels for total cholesterol, triglyceride, Apo B, and systolic blood pressure and were on average older and weighed more than female children with a weak family history of CAD. Male children with a strong family history of CAD had higher average levels of triglycerides and were on average older than male children with a weak family history. In the medium-grained analysis we investigated whether the regression relationships between each intermediate trait and each measure of environmental context was significantly different between children with and without a strong family history of CAD. Our results indicate that children with a strong family history of CAD have a significantly different relationship between their intermediate traits and environmental contexts than children with a weak family history. In the fine-grained analysis, we stratified the sample into age, BMI, and smoking subgroups and tested for mean differences in the intermediate traits between children with and without a strong family history. For seven of the nine intermediate traits we found evidence of significant mean differences between children with and without a strong family history of CAD in particular age and BMI subgroups in nonsmokers that were not expected given the results from separate age-dependent or BMI-dependent marginal analyses. From these analyses, we conclude that the inferences about intermediate biochemical and physiological trait associations with family history of CAD depend on where on the coarse-grain to fine-grain continuum of context dependency the analysis is performed. In many cases, inferences at one level of investigation are different than the inferences made at a coarser or finer level. This study documents the complexity of the associations between intermediate traits and risk of CAD and raises the question of how many models are needed to maximize disease prediction and where these models should fall on the coarse- to fine-grain continuum.
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Affiliation(s)
- S L Kardia
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, USA
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Abstract
OBJECTIVE To assess whether interindividual variation in renal plasma flow or in its response to angiotensin II infusion is associated with interindividual differences in blood pressure in a population-based sample of 287 non-Hispanic whites (143 women and 144 men), aged 20-49.9 years. METHODS After seven days of eating a high-sodium diet (260 mmol/day), the renal plasma flow was determined by measuring the clearance of p-aminohippurate before and after infusion of 3 ng/kg per min angiotensin II. Multiple linear regression methods were used to assess whether measures of the renal plasma flow and of its response to angiotensin II infusion were predictive of systolic or diastolic blood pressures measured prior to administration of the high-sodium diet, on day 6 of the high-sodium diet, or during the renal clearance procedure on day 7 prior to angiotensin II infusion. RESULTS There was some evidence that measures of the renal plasma flow and of its response to angiotensin II infusion during the high-sodium diet were statistically significant predictors of measures of blood pressure in women; there was less evidence for this for blood pressures in men. Interindividual variation in measures of the renal plasma flow and of its response to angiotensin II infusion explained less than 10% of the interindividual variation in any measure of the blood pressure in both sexes. CONCLUSION These results suggest that interindividual variation in renal plasma flow ad in its response to angiotensin II infusion during a high-sodium diet will be of limited utility in elucidating the basis for interindividual differences in blood pressure.
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Affiliation(s)
- S T Turner
- Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
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Kardia SL, Sing CF, Turner ST. The response of renal plasma flow to angiotensin II infusion in a population-based sample and its association with the parental history of essential hypertension. J Hypertens 1997; 15:483-93. [PMID: 9170000 DOI: 10.1097/00004872-199715050-00003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [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: 02/04/2023]
Abstract
BACKGROUND Results from previous studies suggested that a blunted response of renal plasma flow (RPF) to angiotensin II infusion during a high-sodium diet (a phenotype associated with nonmodulation) is an intermediate phenotype for essential hypertension. OBJECTIVE To determine whether RPF traits used to investigate nonmodulation have the characteristics of intermediate traits when examined in a population-based sample of adults aged 20-49.9 years. DESIGN AND METHODS We examined the frequency distribution of baseline RPF and of its response to All infusion using maximum-likelihood commingling analysis in order to investigate the null hypothesis that the distributions of these traits are unimodal. We also examined the null hypothesis that there is no association between these candidate intermediate traits and the parental history of essential hypertension. RESULTS There was some evidence for the commingling of multiple distributions underlying these traits both for women and for men but the commingled distributions overlapped substantially and the inferences about the commingling of distributions were sensitive to the method of RPF measurement, exclusion of outliers, and the method of adjustment for concomitants. There was no statistically significant association between any of the RPF traits and a parental history of essential hypertension. CONCLUSIONS There is not sufficiently strong evidence to advocate the use of this set of intermediate traits to identify high-risk individuals or to relate genetic variation to the variation in risk of essential hypertension within this age range in the population at large.
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Affiliation(s)
- S L Kardia
- Department of Human Genetics, University of Michigan, Ann Arbor, USA
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