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Janani N, Young KA, Kinney G, Strand M, Hokanson JE, Liu Y, Butler T, Austin E. A novel application of data-consistent inversion to overcome spurious inference in genome-wide association studies. Genet Epidemiol 2024. [PMID: 38644517 DOI: 10.1002/gepi.22563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 12/30/2023] [Accepted: 03/27/2024] [Indexed: 04/23/2024]
Abstract
The genome-wide association studies (GWAS) typically use linear or logistic regression models to identify associations between phenotypes (traits) and genotypes (genetic variants) of interest. However, the use of regression with the additive assumption has potential limitations. First, the normality assumption of residuals is the one that is rarely seen in practice, and deviation from normality increases the Type-I error rate. Second, building a model based on such an assumption ignores genetic structures, like, dominant, recessive, and protective-risk cases. Ignoring genetic variants may result in spurious conclusions about the associations between a variant and a trait. We propose an assumption-free model built upon data-consistent inversion (DCI), which is a recently developed measure-theoretic framework utilized for uncertainty quantification. This proposed DCI-derived model builds a nonparametric distribution on model inputs that propagates to the distribution of observed data without the required normality assumption of residuals in the regression model. This characteristic enables the proposed DCI-derived model to cover all genetic variants without emphasizing on additivity of the classic-GWAS model. Simulations and a replication GWAS with data from the COPDGene demonstrate the ability of this model to control the Type-I error rate at least as well as the classic-GWAS (additive linear model) approach while having similar or greater power to discover variants in different genetic modes of transmission.
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Affiliation(s)
- Negar Janani
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, Colorado, USA
| | - Kendra A Young
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA
| | - Greg Kinney
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA
| | - Matthew Strand
- Division of Biostatistics, National Jewish Health, Denver, Colorado, USA
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA
| | - Yaning Liu
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, Colorado, USA
| | - Troy Butler
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, Colorado, USA
| | - Erin Austin
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, Colorado, USA
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Shrine N, Guyatt AL, Erzurumluoglu AM, Jackson VE, Hobbs BD, Melbourne CA, Batini C, Fawcett KA, Song K, Sakornsakolpat P, Li X, Boxall R, Reeve NF, Obeidat M, Zhao JH, Wielscher M, Weiss S, Kentistou KA, Cook JP, Sun BB, Zhou J, Hui J, Karrasch S, Imboden M, Harris SE, Marten J, Enroth S, Kerr SM, Surakka I, Vitart V, Lehtimäki T, Allen RJ, Bakke PS, Beaty TH, Bleecker ER, Bossé Y, Brandsma CA, Chen Z, Crapo JD, Danesh J, DeMeo DL, Dudbridge F, Ewert R, Gieger C, Gulsvik A, Hansell AL, Hao K, Hoffman JD, Hokanson JE, Homuth G, Joshi PK, Joubert P, Langenberg C, Li X, Li L, Lin K, Lind L, Locantore N, Luan J, Mahajan A, Maranville JC, Murray A, Nickle DC, Packer R, Parker MM, Paynton ML, Porteous DJ, Prokopenko D, Qiao D, Rawal R, Runz H, Sayers I, Sin DD, Smith BH, Artigas MS, Sparrow D, Tal-Singer R, Timmers PRHJ, Van den Berge M, Whittaker JC, Woodruff PG, Yerges-Armstrong LM, Troyanskaya OG, Raitakari OT, Kähönen M, Polašek O, Gyllensten U, Rudan I, Deary IJ, Probst-Hensch NM, Schulz H, James AL, Wilson JF, Stubbe B, Zeggini E, Jarvelin MR, Wareham N, Silverman EK, Hayward C, Morris AP, Butterworth AS, Scott RA, Walters RG, Meyers DA, Cho MH, Strachan DP, Hall IP, Tobin MD, Wain LV. Author Correction: New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries. Nat Genet 2024:10.1038/s41588-024-01752-4. [PMID: 38641645 DOI: 10.1038/s41588-024-01752-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Affiliation(s)
- Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anna L Guyatt
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Victoria E Jackson
- Department of Health Sciences, University of Leicester, Leicester, UK
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Kijoung Song
- Target Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | - Phuwanat Sakornsakolpat
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Xingnan Li
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Ruth Boxall
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Nicola F Reeve
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Jing Hua Zhao
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Katherine A Kentistou
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - James P Cook
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Benjamin B Sun
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jian Zhou
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Jennie Hui
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- School of Population Health, The University of Western Australia, Crawley, Western Australia, Australia
- PathWest Laboratory Medicine of WA, Sir Charles Gairdner Hospital, Crawley, Western Australia, Australia
- School of Pathology and Laboratory Medicine, The University of Western Australia, Crawley, Western Australia, Australia
| | - Stefan Karrasch
- Institute of Epidemiology, Helmholtz Zentrum Muenchen-German Research Center for Environmental Health, Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Stefan Enroth
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden
| | - Shona M Kerr
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ida Surakka
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- The National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Richard J Allen
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Per S Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins University School of Public Health, Baltimore, MD, USA
| | - Eugene R Bleecker
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Québec, Canada
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, Canada
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - James D Crapo
- National Jewish Health, Denver, CO, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - John Danesh
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK
- Department of Human Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ralf Ewert
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Anna L Hansell
- Centre for Environmental Health & Sustainability, University of Leicester, Leicester, UK
- UK Small Area Health Statistics Unit, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, Canada
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University, Québec, Canada
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Xuan Li
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Liming Li
- Department of Epidemiology & Biostatistics, Peking University Health Science Center, Beijing, China
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Lars Lind
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University, Uppsala, Sweden
| | | | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Alison Murray
- The Institute of Medical Sciences, Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, UK
| | - David C Nickle
- MRL, Merck & Co., Inc, Kenilworth, NJ, USA
- Gossamer Bio, San Diego, CA, USA
| | - Richard Packer
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Megan L Paynton
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - David J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Heiko Runz
- MRL, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Ian Sayers
- Division of Respiratory Medicine and NIHR-Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Don D Sin
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - María Soler Artigas
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Barcelona, Spain
| | - David Sparrow
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | | | - Paul R H J Timmers
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Maarten Van den Berge
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - John C Whittaker
- Target Sciences - R&D, GSK Medicines Research Centre, Stevenage, UK
| | - Prescott G Woodruff
- UCSF Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
| | | | - Olga G Troyanskaya
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Ozren Polašek
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- University of Split School of Medicine, Split, Croatia
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Nicole M Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Holger Schulz
- Institute of Epidemiology, Helmholtz Zentrum Muenchen-German Research Center for Environmental Health, Neuherberg, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Alan L James
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia, Australia
| | - James F Wilson
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Beate Stubbe
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
| | - Eleftheria Zeggini
- Wellcome Sanger Institute, Hinxton, UK
- Institute of Translational Genomics, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Nick Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Robert A Scott
- Target Sciences - R&D, GSK Medicines Research Centre, Stevenage, UK
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Deborah A Meyers
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, UK
| | - Ian P Hall
- Division of Respiratory Medicine and NIHR-Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK.
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK.
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
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Chen J, Xu Z, Sun L, Yu K, Hersh CP, Boueiz A, Hokanson JE, Sciurba FC, Silverman EK, Castaldi PJ, Batmanghelich K. Deep Learning Integration of Chest Computed Tomography Imaging and Gene Expression Identifies Novel Aspects of COPD. Chronic Obstr Pulm Dis 2023; 10:355-368. [PMID: 37413999 DOI: 10.15326/jcopdf.2023.0399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Rationale Chronic obstructive pulmonary disease (COPD) is characterized by pathologic changes in the airways, lung parenchyma, and persistent inflammation, but the links between lung structural changes and blood transcriptome patterns have not been fully described. Objections The objective of this study was to identify novel relationships between lung structural changes measured by chest computed tomography (CT) and blood transcriptome patterns measured by blood RNA sequencing (RNA-seq). Methods CT scan images and blood RNA-seq gene expression from 1223 participants in the COPD Genetic Epidemiology (COPDGene®) study were jointly analyzed using deep learning to identify shared aspects of inflammation and lung structural changes that we labeled image-expression axes (IEAs). We related IEAs to COPD-related measurements and prospective health outcomes through regression and Cox proportional hazards models and tested them for biological pathway enrichment. Results We identified 2 distinct IEAs: IEAemph which captures an emphysema-predominant process with a strong positive correlation to CT emphysema and a negative correlation to forced expiratory volume in 1 second and body mass index (BMI); and IEAairway which captures an airway-predominant process with a positive correlation to BMI and airway wall thickness and a negative correlation to emphysema. Pathway enrichment analysis identified 29 and 13 pathways significantly associated with IEAemph and IEAairway, respectively (adjusted p<0.001). Conclusions Integration of CT scans and blood RNA-seq data identified 2 IEAs that capture distinct inflammatory processes associated with emphysema and airway-predominant COPD.
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Affiliation(s)
- Junxiang Chen
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Zhonghui Xu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Li Sun
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Ke Yu
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Craig P Hersh
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Adel Boueiz
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States
| | - Frank C Sciurba
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Peter J Castaldi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
- Division of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Kayhan Batmanghelich
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
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Castaldi PJ, Xu Z, Young KA, Hokanson JE, Lynch DA, Humphries SM, Ross JC, Cho MH, Hersh CP, Crapo JD, Strand M, Silverman EK. Heterogeneity and Progression of Chronic Obstructive Pulmonary Disease: Emphysema-Predominant and Non-Emphysema-Predominant Disease. Am J Epidemiol 2023; 192:1647-1658. [PMID: 37160347 DOI: 10.1093/aje/kwad114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 12/20/2022] [Accepted: 05/04/2023] [Indexed: 05/11/2023] Open
Abstract
While variation in emphysema severity between patients with chronic obstructive pulmonary disease (COPD) is well-recognized, clinically applicable definitions of the emphysema-predominant disease (EPD) and non-emphysema-predominant disease (NEPD) subtypes have not been established. To study the clinical relevance of the EPD and NEPD subtypes, we tested the association of these subtypes with prospective decline in forced expiratory volume in 1 second (FEV1) and mortality among 3,427 subjects with Global Initiative for Chronic Obstructive Lung Disease (GOLD) spirometric grade 2-4 COPD at baseline in the Genetic Epidemiology of COPD (COPDGene) Study, an ongoing national multicenter study that started in 2007. NEPD was defined as airflow obstruction with less than 5% computed tomography (CT) quantitative densitometric emphysema at -950 Hounsfield units, and EPD was defined as airflow obstruction with 10% or greater CT emphysema. Mixed-effects models for FEV1 demonstrated larger average annual FEV1 loss in EPD subjects than in NEPD subjects (-10.2 mL/year; P < 0.001), and subtype-specific associations with FEV1 decline were identified. Cox proportional hazards models showed higher risk of mortality among EPD patients versus NEPD patients (hazard ratio = 1.46, 95% confidence interval: 1.34, 1.60; P < 0.001). To determine whether the NEPD/EPD dichotomy is captured by previously described COPDGene subtypes, we used logistic regression and receiver operating characteristic (ROC) curve analysis to predict NEPD/EPD membership using these previous subtype definitions. The analysis generally showed excellent discrimination, with areas under the ROC curve greater than 0.9. The NEPD and EPD COPD subtypes capture important aspects of COPD heterogeneity and are associated with different rates of disease progression and mortality.
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Litkowski EM, Logue MW, Zhang R, Charest BR, Lange EM, Hokanson JE, Lynch JA, Vujkovic M, Phillips LS, Hauger RL, Lange LA, Raghavan S. Mendelian randomization study of diabetes and dementia in the Million Veteran Program. Alzheimers Dement 2023; 19:4367-4376. [PMID: 37417779 PMCID: PMC10592524 DOI: 10.1002/alz.13373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023]
Abstract
INTRODUCTION Diabetes and dementia are diseases of high health-care burden worldwide. Individuals with diabetes have 1.4 to 2.2 times higher risk of dementia. Our objective was to evaluate evidence of causality between these two common diseases. METHODS We conducted a one-sample Mendelian randomization (MR) analysis in the US Department of Veterans Affairs Million Veteran program. The study included 334,672 participants ≥65 years of age with type 2 diabetes and dementia case-control status and genotype data. RESULTS For each standard deviation increase in genetically predicted diabetes, we found increased odds of three dementia diagnoses in non-Hispanic White participants (all-cause: odds ratio [OR] = 1.07 [1.05-1.08], P = 3.40E-18; vascular: OR = 1.11 [1.07-1.15], P = 3.63E-09, Alzheimer's disease [AD]: OR = 1.06 [1.02-1.09], P = 6.84E-04) and non-Hispanic Black participants (all-cause: OR = 1.06 [1.02-1.10], P = 3.66E-03, vascular: OR = 1.11 [1.04-1.19], P = 2.20E-03, AD: OR = 1.12 [1.02-1.23], P = 1.60E-02) but not in Hispanic participants (all P > 0.05). DISCUSSION We found evidence of causality between diabetes and dementia using a one-sample MR study, with access to individual level data, overcoming limitations of prior studies using two-sample MR techniques.
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Affiliation(s)
- Elizabeth M Litkowski
- VA Eastern Colorado Healthcare System, Aurora, Colorado, USA
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Mark W Logue
- National Center for PTSD, Behavioral Sciences Division, VA Boston Healthcare System, Boston, Massachusetts, USA
- Boston University Schools of Medicine and Public Health, Boston, Massachusetts, USA
| | - Rui Zhang
- National Center for PTSD, Behavioral Sciences Division, VA Boston Healthcare System, Boston, Massachusetts, USA
| | | | - Ethan M Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Julie A Lynch
- Salt Lake City VA, VA Informatics & Computing Infrastructure, Salt Lake City, Utah, USA
- School of Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Marijana Vujkovic
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, Pennsylvania, USA
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lawrence S Phillips
- Atlanta VA Health Care System, Decatur, Georgia, USA
- Division of Endocrinology and Metabolism, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Richard L Hauger
- Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, San Diego, California, USA
- Center for Behavior Genetics of Aging, School of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Leslie A Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Sridharan Raghavan
- VA Eastern Colorado Healthcare System, Aurora, Colorado, USA
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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6
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Kavousi M, Bos MM, Barnes HJ, Lino Cardenas CL, Wong D, Lu H, Hodonsky CJ, Landsmeer LPL, Turner AW, Kho M, Hasbani NR, de Vries PS, Bowden DW, Chopade S, Deelen J, Benavente ED, Guo X, Hofer E, Hwang SJ, Lutz SM, Lyytikäinen LP, Slenders L, Smith AV, Stanislawski MA, van Setten J, Wong Q, Yanek LR, Becker DM, Beekman M, Budoff MJ, Feitosa MF, Finan C, Hilliard AT, Kardia SLR, Kovacic JC, Kral BG, Langefeld CD, Launer LJ, Malik S, Hoesein FAAM, Mokry M, Schmidt R, Smith JA, Taylor KD, Terry JG, van der Grond J, van Meurs J, Vliegenthart R, Xu J, Young KA, Zilhão NR, Zweiker R, Assimes TL, Becker LC, Bos D, Carr JJ, Cupples LA, de Kleijn DPV, de Winther M, den Ruijter HM, Fornage M, Freedman BI, Gudnason V, Hingorani AD, Hokanson JE, Ikram MA, Išgum I, Jacobs DR, Kähönen M, Lange LA, Lehtimäki T, Pasterkamp G, Raitakari OT, Schmidt H, Slagboom PE, Uitterlinden AG, Vernooij MW, Bis JC, Franceschini N, Psaty BM, Post WS, Rotter JI, Björkegren JLM, O'Donnell CJ, Bielak LF, Peyser PA, Malhotra R, van der Laan SW, Miller CL. Multi-ancestry genome-wide study identifies effector genes and druggable pathways for coronary artery calcification. Nat Genet 2023; 55:1651-1664. [PMID: 37770635 PMCID: PMC10601987 DOI: 10.1038/s41588-023-01518-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 11/20/2022] [Accepted: 08/29/2023] [Indexed: 09/30/2023]
Abstract
Coronary artery calcification (CAC), a measure of subclinical atherosclerosis, predicts future symptomatic coronary artery disease (CAD). Identifying genetic risk factors for CAC may point to new therapeutic avenues for prevention. Currently, there are only four known risk loci for CAC identified from genome-wide association studies (GWAS) in the general population. Here we conducted the largest multi-ancestry GWAS meta-analysis of CAC to date, which comprised 26,909 individuals of European ancestry and 8,867 individuals of African ancestry. We identified 11 independent risk loci, of which eight were new for CAC and five had not been reported for CAD. These new CAC loci are related to bone mineralization, phosphate catabolism and hormone metabolic pathways. Several new loci harbor candidate causal genes supported by multiple lines of functional evidence and are regulators of smooth muscle cell-mediated calcification ex vivo and in vitro. Together, these findings help refine the genetic architecture of CAC and extend our understanding of the biological and potential druggable pathways underlying CAC.
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Affiliation(s)
- Maryam Kavousi
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Maxime M Bos
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Hanna J Barnes
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Christian L Lino Cardenas
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Doris Wong
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Haojie Lu
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Chani J Hodonsky
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Lennart P L Landsmeer
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Adam W Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Minjung Kho
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Graduate School of Data Science, Seoul National University, Seoul, Republic of Korea
| | - Natalie R Hasbani
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Center at Houston, Houston, TX, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Center at Houston, Houston, TX, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Sandesh Chopade
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- University College London British Heart Foundation Research Accelerator Centre, London, UK
| | - Joris Deelen
- Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Max Planck Institute for Biology of Aging, Cologne, Germany
| | - Ernest Diez Benavente
- Laboratory of Experimental Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Edith Hofer
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | | | - Sharon M Lutz
- Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, MA, USA
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Lotte Slenders
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Icelandic Heart Association, Kopavogur, Iceland
| | - Maggie A Stanislawski
- Department of Biomedical Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Jessica van Setten
- Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Quenna Wong
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Diane M Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marian Beekman
- Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Matthew J Budoff
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Mary F Feitosa
- Department of Genetics, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Chris Finan
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- University College London British Heart Foundation Research Accelerator Centre, London, UK
- Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | | | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jason C Kovacic
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
- St Vincent's Clinical School, University of NSW, Sydney, New South Wales, Australia
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Brian G Kral
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences and Data Science, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Shaista Malik
- Susan Samueli Integrative Health Institute, Department of Medicine, University of California Irvine, Irvine, CA, USA
| | | | - Michal Mokry
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Laboratory of Experimental Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Reinhold Schmidt
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University of Graz, Graz, Austria
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - James G Terry
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeroen van der Grond
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Joyce van Meurs
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rozemarijn Vliegenthart
- Department of Radiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jianzhao Xu
- Department of Biochemistry, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Kendra A Young
- Department of Epidemiology, University of Colorado, Anschutz Medical Campus, Denver, CO, USA
| | | | - Robert Zweiker
- Department of Internal Medicine, Division of Cardiology, Medical University of Graz, Graz, Austria
| | - Themistocles L Assimes
- VA Palo Alto Healthcare System, Palo Alto, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Lewis C Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel Bos
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - J Jeffrey Carr
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - L Adrienne Cupples
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Dominique P V de Kleijn
- Department of Vascular Surgery, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Menno de Winther
- Department of Medical Biochemistry, Experimental Vascular Biology, Amsterdam Cardiovascular Sciences: Atherosclerosis and Ischemic syndromes, Amsterdam Infection and Immunity: Inflammatory diseases, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Hester M den Ruijter
- Laboratory of Experimental Cardiology, Division of Heart and Lungs, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Myriam Fornage
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Barry I Freedman
- Department of Internal Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, School of Public Health, University of Iceland, Reykjavik, Iceland
| | - Aroon D Hingorani
- Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
- University College London British Heart Foundation Research Accelerator Centre, London, UK
| | - John E Hokanson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ivana Išgum
- Image Sciences Institute, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Biomedical Engineering and Physics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - David R Jacobs
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Leslie A Lange
- Department of Biomedical Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Gerard Pasterkamp
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Helena Schmidt
- Gottfried Schatz Research Center (for Cell Signaling, Metabolism and Aging), Medical University of Graz, Graz, Austria
| | - P Eline Slagboom
- Biomedical Data Sciences, Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Meike W Vernooij
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Vascular Surgery, University Medical Center Utrecht and Utrecht University, Utrecht, The Netherlands
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Departments of Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Wendy S Post
- Division of Cardiology, 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
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation (formerly Los Angeles Biomedical Research Institute) at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
- Department of Medicine, Integrated Cardio Metabolic Centre, Karolinska Institutet, Huddinge, Sweden
| | - Christopher J O'Donnell
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Cardiology Section, Department of Medicine, Veterans Affairs Boston Healthcare System, Boston, MA, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Rajeev Malhotra
- Cardiovascular Research Center, Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sander W van der Laan
- Central Diagnostics Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Clint L Miller
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
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7
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Chen Y, Du X, Kuppa A, Feitosa MF, Bielak LF, O'Connell JR, Musani SK, Guo X, Kahali B, Chen VL, Smith AV, Ryan KA, Eirksdottir G, Allison MA, Bowden DW, Budoff MJ, Carr JJ, Chen YDI, Taylor KD, Oliveri A, Correa A, Crudup BF, Kardia SLR, Mosley TH, Norris JM, Terry JG, Rotter JI, Wagenknecht LE, Halligan BD, Young KA, Hokanson JE, Washko GR, Gudnason V, Province MA, Peyser PA, Palmer ND, Speliotes EK. Genome-wide association meta-analysis identifies 17 loci associated with nonalcoholic fatty liver disease. Nat Genet 2023; 55:1640-1650. [PMID: 37709864 PMCID: PMC10918428 DOI: 10.1038/s41588-023-01497-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [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: 08/02/2021] [Accepted: 08/07/2023] [Indexed: 09/16/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is common and partially heritable and has no effective treatments. We carried out a genome-wide association study (GWAS) meta-analysis of imaging (n = 66,814) and diagnostic code (3,584 cases versus 621,081 controls) measured NAFLD across diverse ancestries. We identified NAFLD-associated variants at torsin family 1 member B (TOR1B), fat mass and obesity associated (FTO), cordon-bleu WH2 repeat protein like 1 (COBLL1)/growth factor receptor-bound protein 14 (GRB14), insulin receptor (INSR), sterol regulatory element-binding transcription factor 1 (SREBF1) and patatin-like phospholipase domain-containing protein 2 (PNPLA2), as well as validated NAFLD-associated variants at patatin-like phospholipase domain-containing protein 3 (PNPLA3), transmembrane 6 superfamily 2 (TM6SF2), apolipoprotein E (APOE), glucokinase regulator (GCKR), tribbles homolog 1 (TRIB1), glycerol-3-phosphate acyltransferase (GPAM), mitochondrial amidoxime-reducing component 1 (MARC1), microsomal triglyceride transfer protein large subunit (MTTP), alcohol dehydrogenase 1B (ADH1B), transmembrane channel like 4 (TMC4)/membrane-bound O-acyltransferase domain containing 7 (MBOAT7) and receptor-type tyrosine-protein phosphatase δ (PTPRD). Implicated genes highlight mitochondrial, cholesterol and de novo lipogenesis as causally contributing to NAFLD predisposition. Phenome-wide association study (PheWAS) analyses suggest at least seven subtypes of NAFLD. Individuals in the top 10% and 1% of genetic risk have a 2.5-fold to 6-fold increased risk of NAFLD, cirrhosis and hepatocellular carcinoma. These genetic variants identify subtypes of NAFLD, improve estimates of disease risk and can guide the development of targeted therapeutics.
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Affiliation(s)
- Yanhua Chen
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Xiaomeng Du
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Annapurna Kuppa
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jeffrey R O'Connell
- Department of Endocrinology, Diabetes and Nutrition, University of Maryland - Baltimore, Baltimore, MD, USA
| | - Solomon K Musani
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Bratati Kahali
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Centre for Brain Research, Indian Institute of Science, Bangalore, India
| | - Vincent L Chen
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Kathleen A Ryan
- Department of Endocrinology, Diabetes and Nutrition, University of Maryland - Baltimore, Baltimore, MD, USA
| | | | - Matthew A Allison
- Department of Family Medicine, University of California San Diego, San Diego, CA, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Matthew J Budoff
- Department of Internal Medicine, Lundquist Institute at Harbor-UCLA, Torrance, CA, USA
| | - John Jeffrey Carr
- Department of Radiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yii-Der I Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Antonino Oliveri
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Breland F Crudup
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Sharon L R Kardia
- 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
| | - Jill M Norris
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
| | - James G Terry
- Department of Radiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Lynne E Wagenknecht
- Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Brian D Halligan
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Kendra A Young
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
| | - George R Washko
- Department of Medicine, Division of Pulmonary and Critical Care, Brigham and Women's Hospital, Boston, MA, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Department of Medicine, University of Iceland, Reykjavik, Iceland
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Elizabeth K Speliotes
- Department of Internal Medicine, Division of Gastroenterology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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8
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Labaki WW, Gu T, Murray S, Curtis JL, Wells JM, Bhatt SP, Bon J, Diaz AA, Hersh CP, Wan ES, Kim V, Beaty TH, Hokanson JE, Bowler RP, Arenberg DA, Kazerooni EA, Martinez FJ, Silverman EK, Crapo JD, Make BJ, Regan EA, Han MK. Causes of and Clinical Features Associated with Death in Tobacco Cigarette Users by Lung Function Impairment. Am J Respir Crit Care Med 2023; 208:451-460. [PMID: 37159910 PMCID: PMC10449063 DOI: 10.1164/rccm.202210-1887oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 05/08/2023] [Indexed: 05/11/2023] Open
Abstract
Rationale: Cigarette smoking contributes to the risk of death through different mechanisms. Objectives: To determine how causes of and clinical features associated with death vary in tobacco cigarette users by lung function impairment. Methods: We stratified current and former tobacco cigarette users enrolled in Genetic Epidemiology of Chronic Obstructive Pulmonary Disease (COPDGene) into normal spirometry, PRISm (Preserved Ratio Impaired Spirometry), Global Initiative for Chronic Obstructive Lung Disease (GOLD) 1-2 COPD, and GOLD 3-4 COPD. Deaths were identified via longitudinal follow-up and Social Security Death Index search. Causes of death were adjudicated after a review of death certificates, medical records, and next-of-kin interviews. We tested associations between baseline clinical variables and all-cause mortality using multivariable Cox proportional hazards models. Measurements and Main Results: Over a 10.1-year median follow-up, 2,200 deaths occurred among 10,132 participants (age 59.5 ± 9.0 yr; 46.6% women). Death from cardiovascular disease was most frequent in PRISm (31% of deaths). Lung cancer deaths were most frequent in GOLD 1-2 (18% of deaths vs. 9-11% in other groups). Respiratory deaths outpaced competing causes of death in GOLD 3-4, particularly when BODE index ⩾7. St. George's Respiratory Questionnaire score ⩾25 was associated with higher mortality in all groups: Hazard ratio (HR), 1.48 (1.20-1.84) normal spirometry; HR, 1.40 (1.05-1.87) PRISm; HR, 1.80 (1.49-2.17) GOLD 1-2; HR, 1.65 (1.26-2.17) GOLD 3-4. History of respiratory exacerbations was associated with higher mortality in GOLD 1-2 and GOLD 3-4, quantitative emphysema in GOLD 1-2, and airway wall thickness in PRISm and GOLD 3-4. Conclusions: Leading causes of death vary by lung function impairment in tobacco cigarette users. Worse respiratory-related quality of life is associated with all-cause mortality regardless of lung function.
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Affiliation(s)
| | - Tian Gu
- Department of Biostatistics, T.H. Chan School of Public Health
| | | | - Jeffrey L. Curtis
- Division of Pulmonary and Critical Care Medicine
- Medical Service, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan
| | - J. Michael Wells
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Surya P. Bhatt
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jessica Bon
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
- Medical Service, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania
| | | | - Craig P. Hersh
- Division of Pulmonary and Critical Care Medicine, and
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Harvard University, Boston, Massachusetts
| | - Emily S. Wan
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Harvard University, Boston, Massachusetts
- Veterans Affairs Boston Healthcare System, Boston, Massachusetts
| | - Victor Kim
- Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - John E. Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | | | | | - Ella A. Kazerooni
- Division of Pulmonary and Critical Care Medicine
- Department of Radiology, University of Michigan, Ann Arbor, Michigan
| | - Fernando J. Martinez
- Division of Pulmonary and Critical Care Medicine, Weill Cornell Medical College, New York, New York
| | - Edwin K. Silverman
- Division of Pulmonary and Critical Care Medicine, and
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Harvard University, Boston, Massachusetts
| | - James D. Crapo
- Division of Pulmonary, Critical Care and Sleep Medicine and
| | - Barry J. Make
- Division of Pulmonary, Critical Care and Sleep Medicine and
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9
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Arjomandi M, Zeng S, Chen J, Bhatt SP, Abtin F, Barjaktarevic I, Barr RG, Bleecker ER, Buhr RG, Criner GJ, Comellas AP, Couper DJ, Curtis JL, Dransfield MT, Fortis S, Han MK, Hansel NN, Hoffman EA, Hokanson JE, Kaner RJ, Kanner RE, Krishnan JA, Labaki WW, Lynch DA, Ortega VE, Peters SP, Woodruff PG, Cooper CB, Bowler RP, Paine III R, Rennard SI, Tashkin DP. Changes in Lung Volumes with Spirometric Disease Progression in COPD. Chronic Obstr Pulm Dis 2023; 10:270-285. [PMID: 37199719 PMCID: PMC10484496 DOI: 10.15326/jcopdf.2022.0363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/12/2023] [Indexed: 05/19/2023]
Abstract
Background Abnormal lung volumes representing air trapping identify the subset of smokers with preserved spirometry who develop spirometric chronic obstructive pulmonary disease (COPD) and adverse outcomes. However, how lung volumes evolve in early COPD as airflow obstruction develops remains unclear. Methods To establish how lung volumes change with the development of spirometric COPD, we examined lung volumes from the pulmonary function data (seated posture) available in the U.S. Department of Veterans Affairs electronic health records (n=71,356) and lung volumes measured by computed tomography (supine posture) available from the COPD Genetic Epidemiology (COPDGene®) study (n=7969) and the SubPopulations and InterMediate Outcome Measures In COPD Study (SPIROMICS) (n=2552) cohorts, and studied their cross-sectional distributions and longitudinal changes across the airflow obstruction spectrum. Patients with preserved ratio-impaired spirometry (PRISm) were excluded from this analysis. Results Lung volumes from all 3 cohorts showed similar patterns of distributions and longitudinal changes with worsening airflow obstruction. The distributions for total lung capacity (TLC), vital capacity (VC), and inspiratory capacity (IC) and their patterns of change were nonlinear and included different phases. When stratified by airflow obstruction using Global initiative for chronic Obstructive Lung Disease (GOLD) stages, patients with GOLD 1 (mild) COPD had larger lung volumes (TLC, VC, IC) compared to patients with GOLD 0 (smokers with preserved spirometry) or GOLD 2 (moderate) disease. In longitudinal follow-up of baseline GOLD 0 patients who progressed to spirometric COPD, those with an initially higher TLC and VC developed mild obstruction (GOLD 1) while those with an initially lower TLC and VC developed moderate obstruction (GOLD 2). Conclusions In COPD, TLC, and VC have biphasic distributions, change in nonlinear fashions as obstruction worsens, and could differentiate those GOLD 0 patients at risk for more rapid spirometric disease progression.
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Affiliation(s)
- Mehrdad Arjomandi
- San Francisco Veterans Affairs Healthcare System, San Francisco, California, United States
- Department of Medicine, University of California, San Francisco, California, United States
| | - Siyang Zeng
- San Francisco Veterans Affairs Healthcare System, San Francisco, California, United States
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, United States
| | - Jianhong Chen
- San Francisco Veterans Affairs Healthcare System, San Francisco, California, United States
- Department of Medicine, University of California, San Francisco, California, United States
| | - Surya P. Bhatt
- University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Fereidoun Abtin
- Department of Medicine, University of California, Los Angeles, California, United States
| | - Igor Barjaktarevic
- Department of Medicine, University of California, Los Angeles, California, United States
| | - R. Graham Barr
- Columbia-Presbyterian Medical Center, New York, New York, United States
| | - Eugene R. Bleecker
- University of Arizona, College of Medicine, Tucson, Arizona, United States
| | - Russell G. Buhr
- Department of Medicine, University of California, Los Angeles, California, United States
| | | | | | - David J. Couper
- University of North Carolina, Chapel Hill, North Carolina, United States
| | - Jeffrey L. Curtis
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States
- Medical Service, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan, United States
| | | | | | - MeiLan K. Han
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States
| | - Nadia N. Hansel
- Department of Medicine, Johns Hopkins University, Baltimore, United States
| | | | - John E. Hokanson
- Department of Epidemiology, School of Public Health, University of Colorado, United States
| | - Robert J. Kaner
- Weill Cornell Medical Center, New York, New York, United States
| | | | | | - Wassim W. Labaki
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States
| | - David A. Lynch
- Department of Radiology, National Jewish Health Systems, Denver, Colorado, United States
| | | | - Stephen P. Peters
- Wake Forest School of Medicine, Winston-Salem, North Carolina, United States
| | - Prescott G. Woodruff
- Department of Medicine, University of California, San Francisco, California, United States
| | - Christopher B. Cooper
- Department of Medicine, University of California, Los Angeles, California, United States
| | - Russell P. Bowler
- Department of Medicine, National Jewish Health Systems, Denver, Colorado, United States
| | - Robert Paine III
- University of Utah, Salt Lake City, Utah, United States
- Department of Medicine, National Jewish Health Systems, Denver, Colorado, United States
| | | | - Donald P. Tashkin
- Columbia-Presbyterian Medical Center, New York, New York, United States
| | - the COPDGene and SPIROMICS Investigators.
- San Francisco Veterans Affairs Healthcare System, San Francisco, California, United States
- Department of Medicine, University of California, San Francisco, California, United States
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, United States
- University of Alabama at Birmingham, Birmingham, Alabama, United States
- Department of Medicine, University of California, Los Angeles, California, United States
- Columbia-Presbyterian Medical Center, New York, New York, United States
- University of Arizona, College of Medicine, Tucson, Arizona, United States
- Temple University, Philadelphia, Pennsylvania, United States
- University of Iowa, Iowa City, Iowa, United States
- University of North Carolina, Chapel Hill, North Carolina, United States
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States
- Medical Service, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan, United States
- Department of Medicine, Johns Hopkins University, Baltimore, United States
- Department of Epidemiology, School of Public Health, University of Colorado, United States
- Weill Cornell Medical Center, New York, New York, United States
- University of Utah, Salt Lake City, Utah, United States
- University of Illinois at Chicago, Chicago, Illinois, United States
- Department of Radiology, National Jewish Health Systems, Denver, Colorado, United States
- Mayo Clinic, Scottsdale, Arizona, United States
- Wake Forest School of Medicine, Winston-Salem, North Carolina, United States
- Department of Medicine, National Jewish Health Systems, Denver, Colorado, United States
- University of Nebraska Medical Center, Omaha, Nebraska, United States
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10
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Li Y, Schmiege SJ, Anderson H, Richmond NE, Young KA, Hokanson JE, Rennard SI, Crume TL, Austin E, Pratte KA, Conway R, Kinney GL. Longitudinal Assessment of Multimorbidity Medication Patterns among Smokers in the COPDGene Cohort. Medicina (Kaunas) 2023; 59:medicina59050976. [PMID: 37241208 DOI: 10.3390/medicina59050976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/08/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023]
Abstract
Background and objectives: Chronic obstructive pulmonary disease (COPD) is usually comorbid with other chronic diseases. We aimed to assess the multimorbidity medication patterns and explore if the patterns are similar for phase 1 (P1) and 5-year follow-up phase 2 (P2) in the COPDGene cohort. Materials and Methods: A total of 5564 out of 10,198 smokers from the COPDGene cohort who completed 2 visits, P1 and P2 visits, with complete medication use history were included in the study. We conducted latent class analysis (LCA) among the 27 categories of chronic disease medications, excluding COPD treatments and cancer medications at P1 and P2 separately. The best number of LCA classes was determined through both statistical fit and interpretation of the patterns. Results: We found four classes of medication patterns at both phases. LCA showed that both phases shared similar characteristics in their medication patterns: LC0: low medication; LC1: hypertension (HTN) or cardiovascular disease (CVD)+high cholesterol (Hychol) medication predominant; LC2: HTN/CVD+type 2 diabetes (T2D) +Hychol medication predominant; LC3: Hychol medication predominant. Conclusions: We found similar multimorbidity medication patterns among smokers at P1 and P2 in the COPDGene cohort, which provides an understanding of how multimorbidity medication clustered and how different chronic diseases combine in smokers.
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Affiliation(s)
- Yisha Li
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sarah J Schmiege
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Heather Anderson
- Department of Clinical Pharmacy, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nicole E Richmond
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kendra A Young
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Stephen I Rennard
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Tessa L Crume
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Erin Austin
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA
| | - Katherine A Pratte
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, CO 80206, USA
| | - Rebecca Conway
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Gregory L Kinney
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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11
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Litkowski EM, Logue MW, Zhang R, Charest BR, Lange EM, Hokanson JE, Lynch JA, Vujkovic M, Phillips LS, Hauger RL, Lange LA, Raghavan S. Mendelian randomization study of diabetes and dementia in the Million Veteran Program. medRxiv 2023:2023.03.07.23286526. [PMID: 36945581 PMCID: PMC10029030 DOI: 10.1101/2023.03.07.23286526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
INTRODUCTION Diabetes and dementia are diseases of high healthcare burden worldwide. Individuals with diabetes have 1.4 to 2.2 times higher risk of dementia. Our objective was to evaluate evidence of causality between these two common diseases. METHODS We conducted a one-sample Mendelian randomization (MR) analysis in the U.S. Department of Veterans Affairs Million Veteran program. The study included 334,672 participants ≥65 years of age with type 2 diabetes and dementia case-control status and genotype data. RESULTS For each standard deviation increase in genetically-predicted diabetes, we found increased odds of three dementia diagnoses in non-Hispanic White participants (all-cause: OR=1.07[1.05-1.08], P =3.40E-18; vascular: OR=1.11[1.07-1.15], P =3.63E-09, Alzheimer's: OR=1.06[1.02-1.09], P =6.84E-04) and non-Hispanic Black participants (all-cause: OR=1.06[1.02-1.10], P =3.66E-03, vascular: OR=1.11[1.04-1.19], P =2.20E-03, Alzheimer's: OR=1.12 [1.02-1.23], P =1.60E-02) but not in Hispanic participants (all P >.05). DISCUSSION We found evidence of causality between diabetes and dementia using a one-sample MR study, with access to individual level data, overcoming limitations of prior studies utilizing two-sample MR techniques.
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Affiliation(s)
- Elizabeth M Litkowski
- VA Eastern Colorado Healthcare System, Aurora, CO, 80045 USA
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Mark W Logue
- National Center for PTSD, Behavioral Sciences Division, VA Boston Healthcare System, Boston, MA, 02301, USA
- Boston University Schools of Medicine and Public Health, Boston, MA, 02118, USA
| | - Rui Zhang
- National Center for PTSD, Behavioral Sciences Division, VA Boston Healthcare System, Boston, MA, 02301, USA
| | | | - Ethan M Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Julie A Lynch
- Salt Lake City VA, VA Informatics & Computing Infrastructure, Salt Lake City, UT, 84148, USA
- University of Utah, School of Medicine, Salt Lake City, UT, 84132, USA
| | - Marijana Vujkovic
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
- University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lawrence S Phillips
- Atlanta VA Health Care System, Decatur, GA, 30033, USA
- Division of Endocrinology and Metabolism, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30307, USA
| | - Richard L Hauger
- Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, San Diego, CA, 92161, USA
- Center for Behavior Genetics of Aging, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Leslie A Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Sridharan Raghavan
- VA Eastern Colorado Healthcare System, Aurora, CO, 80045 USA
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
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12
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Chen F, Wang X, Jang SK, Quach BC, Weissenkampen JD, Khunsriraksakul C, Yang L, Sauteraud R, Albert CM, Allred NDD, Arnett DK, Ashley-Koch AE, Barnes KC, Barr RG, Becker DM, Bielak LF, Bis JC, Blangero J, Boorgula MP, Chasman DI, Chavan S, Chen YDI, Chuang LM, Correa A, Curran JE, David SP, Fuentes LDL, Deka R, Duggirala R, Faul JD, Garrett ME, Gharib SA, Guo X, Hall ME, Hawley NL, He J, Hobbs BD, Hokanson JE, Hsiung CA, Hwang SJ, Hyde TM, Irvin MR, Jaffe AE, Johnson EO, Kaplan R, Kardia SLR, Kaufman JD, Kelly TN, Kleinman JE, Kooperberg C, Lee IT, Levy D, Lutz SM, Manichaikul AW, Martin LW, Marx O, McGarvey ST, Minster RL, Moll M, Moussa KA, Naseri T, North KE, Oelsner EC, Peralta JM, Peyser PA, Psaty BM, Rafaels N, Raffield LM, Reupena MS, Rich SS, Rotter JI, Schwartz DA, Shadyab AH, Sheu WHH, Sims M, Smith JA, Sun X, Taylor KD, Telen MJ, Watson H, Weeks DE, Weir DR, Yanek LR, Young KA, Young KL, Zhao W, Hancock DB, Jiang B, Vrieze S, Liu DJ. Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing. Nat Genet 2023; 55:291-300. [PMID: 36702996 PMCID: PMC9925385 DOI: 10.1038/s41588-022-01282-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/08/2022] [Indexed: 01/27/2023]
Abstract
Most transcriptome-wide association studies (TWASs) so far focus on European ancestry and lack diversity. To overcome this limitation, we aggregated genome-wide association study (GWAS) summary statistics, whole-genome sequences and expression quantitative trait locus (eQTL) data from diverse ancestries. We developed a new approach, TESLA (multi-ancestry integrative study using an optimal linear combination of association statistics), to integrate an eQTL dataset with a multi-ancestry GWAS. By exploiting shared phenotypic effects between ancestries and accommodating potential effect heterogeneities, TESLA improves power over other TWAS methods. When applied to tobacco use phenotypes, TESLA identified 273 new genes, up to 55% more compared with alternative TWAS methods. These hits and subsequent fine mapping using TESLA point to target genes with biological relevance. In silico drug-repurposing analyses highlight several drugs with known efficacy, including dextromethorphan and galantamine, and new drugs such as muscle relaxants that may be repurposed for treating nicotine addiction.
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Affiliation(s)
- Fang Chen
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Xingyan Wang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Seon-Kyeong Jang
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | | | - J Dylan Weissenkampen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychology, Penn State College of Medicine, Hershey, PA, USA
| | | | - Lina Yang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Renan Sauteraud
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Christine M Albert
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Donna K Arnett
- College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
- Duke Comprehensive Sickle Cell Center, Duke University Medical Center, Durham, NC, USA
| | - Kathleen C Barnes
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - R Graham Barr
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Diane M Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Joshua C Bis
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Meher Preethi Boorgula
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sameer Chavan
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Yii-Der I Chen
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Lee-Ming Chuang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Adolfo Correa
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
| | - Joanne E Curran
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Sean P David
- University of Chicago, Chicago, IL, USA
- NorthShore University Health System, Evanston, IL, USA
| | - Lisa de Las Fuentes
- Department of Medicine, Division of Biostatistics and Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, USA
| | - Ranjan Deka
- Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Ravindranath Duggirala
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Jessica D Faul
- Institute for Social Research, Survey Research Center, University of Michigan, Ann Arbor, MI, USA
| | - Melanie E Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Sina A Gharib
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Computational Medicine Core at Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Xiuqing Guo
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Michael E Hall
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Nicola L Hawley
- Department of Epidemiology (Chronic Disease), School of Public Health, Yale University, New Haven, CT, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Brian D Hobbs
- Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Chao A Hsiung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Shih-Jen Hwang
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- The Framingham Heart Study, Framingham, MA, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Mental Health and Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Human Genetics and Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, The Bronx, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Joel D Kaufman
- Departments of Environmental & Occupational Health Sciences, Medicine, and Epidemiology, University of Washington Seattle, Seattle, WA, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - I-Te Lee
- Department of Internal Medicine, Division of Endocrinology and Metabolism, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Daniel Levy
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sharon M Lutz
- Department of Population Medicine, Harvard Pilgrim Health Care, Boston, MA, USA
| | - Ani W Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Lisa W Martin
- Division of Cardiology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Olivia Marx
- Department of Biomedical Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Stephen T McGarvey
- Department of Epidemiology, International Health Institute, Brown University School of Public Health, Providence, RI, USA
| | - Ryan L Minster
- Department of Human Genetics and Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew Moll
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Karine A Moussa
- Penn State Huck Institutes of Life Sciences, Penn State College of Medicine, University Park, PA, USA
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elizabeth C Oelsner
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Juan M Peralta
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Bruce M Psaty
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Nicholas Rafaels
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | - Aladdin H Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | | | - Mario Sims
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Institute for Social Research, Survey Research Center, 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
| | - Kent D Taylor
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marilyn J Telen
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Harold Watson
- Faculty of Medical Sciences, University of the West Indies, Cave Hill Campus, Barbados
| | - Daniel E Weeks
- Department of Human Genetics and Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - David R Weir
- Institute for Social Research, Survey Research Center, University of Michigan, Ann Arbor, MI, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kendra A Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Institute for Social Research, Survey Research Center, University of Michigan, Ann Arbor, MI, USA
| | | | - Bibo Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA.
| | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA.
| | - Dajiang J Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA.
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Saunders GRB, Wang X, Chen F, Jang SK, Liu M, Wang C, Gao S, Jiang Y, Khunsriraksakul C, Otto JM, Addison C, Akiyama M, Albert CM, Aliev F, Alonso A, Arnett DK, Ashley-Koch AE, Ashrani AA, Barnes KC, Barr RG, Bartz TM, Becker DM, Bielak LF, Benjamin EJ, Bis JC, Bjornsdottir G, Blangero J, Bleecker ER, Boardman JD, Boerwinkle E, Boomsma DI, Boorgula MP, Bowden DW, Brody JA, Cade BE, Chasman DI, Chavan S, Chen YDI, Chen Z, Cheng I, Cho MH, Choquet H, Cole JW, Cornelis MC, Cucca F, Curran JE, de Andrade M, Dick DM, Docherty AR, Duggirala R, Eaton CB, Ehringer MA, Esko T, Faul JD, Fernandes Silva L, Fiorillo E, Fornage M, Freedman BI, Gabrielsen ME, Garrett ME, Gharib SA, Gieger C, Gillespie N, Glahn DC, Gordon SD, Gu CC, Gu D, Gudbjartsson DF, Guo X, Haessler J, Hall ME, Haller T, Harris KM, He J, Herd P, Hewitt JK, Hickie I, Hidalgo B, Hokanson JE, Hopfer C, Hottenga J, Hou L, Huang H, Hung YJ, Hunter DJ, Hveem K, Hwang SJ, Hwu CM, Iacono W, Irvin MR, Jee YH, Johnson EO, Joo YY, Jorgenson E, Justice AE, Kamatani Y, Kaplan RC, Kaprio J, Kardia SLR, Keller MC, Kelly TN, Kooperberg C, Korhonen T, Kraft P, Krauter K, Kuusisto J, Laakso M, Lasky-Su J, Lee WJ, Lee JJ, Levy D, Li L, Li K, Li Y, Lin K, Lind PA, Liu C, Lloyd-Jones DM, Lutz SM, Ma J, Mägi R, Manichaikul A, Martin NG, Mathur R, Matoba N, McArdle PF, McGue M, McQueen MB, Medland SE, Metspalu A, Meyers DA, Millwood IY, Mitchell BD, Mohlke KL, Moll M, Montasser ME, Morrison AC, Mulas A, Nielsen JB, North KE, Oelsner EC, Okada Y, Orrù V, Palmer ND, Palviainen T, Pandit A, Park SL, Peters U, Peters A, Peyser PA, Polderman TJC, Rafaels N, Redline S, Reed RM, Reiner AP, Rice JP, Rich SS, Richmond NE, Roan C, Rotter JI, Rueschman MN, Runarsdottir V, Saccone NL, Schwartz DA, Shadyab AH, Shi J, Shringarpure SS, Sicinski K, Skogholt AH, Smith JA, Smith NL, Sotoodehnia N, Stallings MC, Stefansson H, Stefansson K, Stitzel JA, Sun X, Syed M, Tal-Singer R, Taylor AE, Taylor KD, Telen MJ, Thai KK, Tiwari H, Turman C, Tyrfingsson T, Wall TL, Walters RG, Weir DR, Weiss ST, White WB, Whitfield JB, Wiggins KL, Willemsen G, Willer CJ, Winsvold BS, Xu H, Yanek LR, Yin J, Young KL, Young KA, Yu B, Zhao W, Zhou W, Zöllner S, Zuccolo L, Batini C, Bergen AW, Bierut LJ, David SP, Gagliano Taliun SA, Hancock DB, Jiang B, Munafò MR, Thorgeirsson TE, Liu DJ, Vrieze S. Genetic diversity fuels gene discovery for tobacco and alcohol use. Nature 2022; 612:720-724. [PMID: 36477530 PMCID: PMC9771818 DOI: 10.1038/s41586-022-05477-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 10/25/2022] [Indexed: 12/12/2022]
Abstract
Tobacco and alcohol use are heritable behaviours associated with 15% and 5.3% of worldwide deaths, respectively, due largely to broad increased risk for disease and injury1-4. These substances are used across the globe, yet genome-wide association studies have focused largely on individuals of European ancestries5. Here we leveraged global genetic diversity across 3.4 million individuals from four major clines of global ancestry (approximately 21% non-European) to power the discovery and fine-mapping of genomic loci associated with tobacco and alcohol use, to inform function of these loci via ancestry-aware transcriptome-wide association studies, and to evaluate the genetic architecture and predictive power of polygenic risk within and across populations. We found that increases in sample size and genetic diversity improved locus identification and fine-mapping resolution, and that a large majority of the 3,823 associated variants (from 2,143 loci) showed consistent effect sizes across ancestry dimensions. However, polygenic risk scores developed in one ancestry performed poorly in others, highlighting the continued need to increase sample sizes of diverse ancestries to realize any potential benefit of polygenic prediction.
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Affiliation(s)
| | - Xingyan Wang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Fang Chen
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Seon-Kyeong Jang
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Mengzhen Liu
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Chen Wang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Shuang Gao
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Yu Jiang
- Department of Epidemiology & Population Health at Stanford University, Stanford, CA, USA
| | | | - Jacqueline M Otto
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Clifton Addison
- Jackson Heart Study (JHS) Graduate Training and Education Center (GTEC), Department of Epidemiology and Biostatistics, School of Public Health, Jackson State University, Jackson, MS, USA
| | - Masato Akiyama
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Ocular Pathology and Imaging Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Christine M Albert
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Fazil Aliev
- Department of Psychiatry, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Alvaro Alonso
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Donna K Arnett
- Dean's Office and Department of Epidemiology, College of Public Health, University of Kentucky, Lexington, KY, USA
| | - Allison E Ashley-Koch
- Department of Medicine and Duke Comprehensive Sickle Cell Center, Duke University School of Medicine, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Aneel A Ashrani
- Division of Hematology, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Tempus, Chicago, IL, USA
| | - R Graham Barr
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Diane M Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Emelia J Benjamin
- Department of Medicine, Boston Medical Center, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | | | - Jason D Boardman
- Institute of Behavioral Science, University of Colorado Boulder, Boulder, CO, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Dorret I Boomsma
- Netherlands Twin Register, Dept Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Meher Preethi Boorgula
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sameer Chavan
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Zhengming Chen
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Iona Cheng
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Hélène Choquet
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, USA
| | - John W Cole
- Department of Neurology, Baltimore Veterans Affairs Medical Center, Baltimore, MD, USA
- Division of Vascular Neurology, Department of Neurology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Marilyn C Cornelis
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Mariza de Andrade
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Danielle M Dick
- Department of Psychiatry, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Anna R Docherty
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Virginia, USA
- Huntsman Mental Health Institute, Salt Lake City, UT, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Charles B Eaton
- Department of Family Medicine, Brown University, Providence, RI, USA
| | - Marissa A Ehringer
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Tõnu Esko
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Lilian Fernandes Silva
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Barry I Freedman
- Department of Internal Medicine-Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Maiken E Gabrielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Melanie E Garrett
- Department of Medicine and Duke Comprehensive Sickle Cell Center, Duke University School of Medicine, Durham, NC, USA
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sina A Gharib
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
- Center for Lung Biology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nathan Gillespie
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Virginia, USA
| | - David C Glahn
- Department of Psychiatry & Behavioral Sciences, Boston Children's Hospital & Harvard Medical School, Boston, MA, USA
| | - Scott D Gordon
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Charles C Gu
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Dongfeng Gu
- Department of Epidemiology and Key Laboratory of Cardiovascular Epidemiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jeffrey Haessler
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael E Hall
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Toomas Haller
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Kathleen Mullan Harris
- Department of Sociology and the Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA
| | - Jiang He
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
- Translational Sciences Institute, Tulane University, New Orleans, LA, USA
| | - Pamela Herd
- McCourt School of Public Policy, Georgetown University, Washington, DC, USA
| | - John K Hewitt
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department Of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Ian Hickie
- Youth Mental Health & Technology Team, Brain and Mind Centre, University of Sydney, Sydney, Australia
| | - Bertha Hidalgo
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Christian Hopfer
- Department of Psychiatry, University of Colorado Anschutz Medical Center, Denver, CO, USA
| | - JoukeJan Hottenga
- Netherlands Twin Register, Dept Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Hongyan Huang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yi-Jen Hung
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, Taiwan
| | - David J Hunter
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Center, Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Research, Innovation and Education, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Shih-Jen Hwang
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Chii-Min Hwu
- Section of Endocrinology and Metabolism, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - William Iacono
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yon Ho Jee
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
- Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Yoonjung Y Joo
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Institute of Data Science, Korea University, Seoul, South Korea
| | | | - Anne E Justice
- Department of Population Health Sciences, Geisinger, Danville, PA, USA
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Robert C Kaplan
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland - FIMM, University of Helsinki, Helsinki, Finland
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Matthew C Keller
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department Of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Tanika N Kelly
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
- Translational Sciences Institute, Tulane University, New Orleans, LA, USA
| | - Charles Kooperberg
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tellervo Korhonen
- Institute for Molecular Medicine Finland - FIMM, University of Helsinki, Helsinki, Finland
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kenneth Krauter
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
- Center for Medicine and Clinical Research, Kuopio University Hospital, Kuopio, Finland
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Jessica Lasky-Su
- Brigham and Women's Hospital, Department of Medicine, Channing Division of Network Medicine, Boston, MA, USA
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung City, Taiwan
| | - James J Lee
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Kevin Li
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Yuqing Li
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA, USA
| | - Kuang Lin
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Penelope A Lind
- Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Chunyu Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Donald M Lloyd-Jones
- Departments of Preventive Medicine, Medicine, and Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sharon M Lutz
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Department of Biostatics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jiantao Ma
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Division of Nutrition Epidemiology and Data Science, Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
| | - Reedik Mägi
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Ravi Mathur
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Nana Matoba
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Genetics, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Patrick F McArdle
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Matthew B McQueen
- Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Sarah E Medland
- Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | | | - Iona Y Millwood
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Braxton D Mitchell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Matthew Moll
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - May E Montasser
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Antonella Mulas
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Jonas B Nielsen
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elizabeth C Oelsner
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Yukinori Okada
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland - FIMM, University of Helsinki, Helsinki, Finland
| | - Anita Pandit
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - S Lani Park
- Population Sciences of the Pacific Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig Maximilians University Munich, Munich, Germany
- German Centre for Cardiovascular Research, DZHK, Partner Site Munich, Munich, Germany
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Tinca J C Polderman
- Department of Clinical Developmental Psychology, Vrije Universiteit, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry, Amsterdam UMC, Amsterdam, The Netherlands
| | - Nicholas Rafaels
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Robert M Reed
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alex P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - John P Rice
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Nicole E Richmond
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Carol Roan
- Center for Demography of Health and Aging, University of Wisconsin-Madison, Madison, WI, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Michael N Rueschman
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Nancy L Saccone
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - David A Schwartz
- Division of Pulmonary Sciences and Critical Care Medicine; Department of Medicine and Immunology, University of Colorado, Aurora, CO, USA
| | - Aladdin H Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Kamil Sicinski
- Center for Demography of Health and Aging, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne Heidi Skogholt
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Michael C Stallings
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department Of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | | | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Jerry A Stitzel
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Xiao Sun
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
| | - Moin Syed
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | | | - Amy E Taylor
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, UK
- National Institute for Health Research Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marilyn J Telen
- Department of Medicine and Duke Comprehensive Sickle Cell Center, Duke University School of Medicine, Durham, NC, USA
| | - Khanh K Thai
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, USA
| | - Hemant Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Constance Turman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Tamara L Wall
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Robin G Walters
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Scott T Weiss
- Brigham and Women's Hospital, Department of Medicine, Channing Division of Network Medicine, Boston, MA, USA
| | - Wendy B White
- Jackson Heart Study Undergraduate Training and Education Center, Tougaloo College, Tougaloo, MS, USA
| | - John B Whitfield
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Kerri L Wiggins
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Gonneke Willemsen
- Netherlands Twin Register, Dept Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Bendik S Winsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Huichun Xu
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jie Yin
- Kaiser Permanente Northern California (KPNC), Division of Research, Oakland, CA, USA
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kendra A Young
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Bing Yu
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Wei Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Sebastian Zöllner
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Luisa Zuccolo
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Health Data Science Centre, Fondazione Human Technopole, Milan, Italy
| | - Chiara Batini
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Andrew W Bergen
- Oregon Research Institute, Springfield, OR, USA
- BioRealm, LLC, Walnut, CA, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Sean P David
- Outcomes Research Network & Department of Family Medicine, NorthShore University HealthSystem, Evanston, IL, USA
- Department of Family Medicine, University of Chicago, Chicago, IL, USA
| | - Sarah A Gagliano Taliun
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
- Department of Neurosciences, Université de Montréal, Montréal, Québec, Canada
- Research Centre, Montréal Heart Institute, Montréal, Québec, Canada
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Bibo Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Marcus R Munafò
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, UK
- National Institute for Health Research Biomedical Research Centre at the University Hospitals Bristol NHS Foundation Trust and the University of Bristol, Bristol, UK
- School of Psychological Science, University of Bristol, Bristol, UK
| | | | - Dajiang J Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA.
| | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA.
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14
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Wilson AC, Bon JM, Mason S, Diaz AA, Lutz SM, Estepar RSJ, Kinney GL, Hokanson JE, Rennard SI, Casaburi R, Bhatt SP, Irvin MR, Hersh CP, Dransfield MT, Washko GR, Regan EA, McDonald ML. Increased chest CT derived bone and muscle measures capture markers of improved morbidity and mortality in COPD. Respir Res 2022; 23:311. [PMID: 36376854 PMCID: PMC9664607 DOI: 10.1186/s12931-022-02237-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/03/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is a disease of accelerated aging and is associated with comorbid conditions including osteoporosis and sarcopenia. These extrapulmonary conditions are highly prevalent yet frequently underdiagnosed and overlooked by pulmonologists in COPD treatment and management. There is evidence supporting a role for bone-muscle crosstalk which may compound osteoporosis and sarcopenia risk in COPD. Chest CT is commonly utilized in COPD management, and we evaluated its utility to identify low bone mineral density (BMD) and reduced pectoralis muscle area (PMA) as surrogates for osteoporosis and sarcopenia. We then tested whether BMD and PMA were associated with morbidity and mortality in COPD. METHODS BMD and PMA were analyzed from chest CT scans of 8468 COPDGene participants with COPD and controls (smoking and non-smoking). Multivariable regression models tested the relationship of BMD and PMA with measures of function (6-min walk distance (6MWD), handgrip strength) and disease severity (percent emphysema and lung function). Multivariable Cox proportional hazards models were used to evaluate the relationship between sex-specific quartiles of BMD and/or PMA derived from non-smoking controls with all-cause mortality. RESULTS COPD subjects had significantly lower BMD and PMA compared with controls. Higher BMD and PMA were associated with increased physical function and less disease severity. Participants with the highest BMD and PMA quartiles had a significantly reduced mortality risk (36% and 46%) compared to the lowest quartiles. CONCLUSIONS These findings highlight the potential for CT-derived BMD and PMA to characterize osteoporosis and sarcopenia using equipment available in the pulmonary setting.
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Affiliation(s)
- Ava C Wilson
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, 701, 19th Street S., LHRB 440, Birmingham, AL, 35233, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jessica M Bon
- Division of Pulmonary, Allergy and Critical Medicine, University of Pittsburgh Health System, Pittsburgh, PA, USA
- VA Pittsburgh Health System, Pittsburgh, PA, USA
| | - Stephanie Mason
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Alejandro A Diaz
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sharon M Lutz
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Raul San Jose Estepar
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gregory L Kinney
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Richard Casaburi
- Rehabilitation Clinical Trials Center, Lundquist Institute for Biomedical Innovation at Harbor Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Surya P Bhatt
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, 701, 19th Street S., LHRB 440, Birmingham, AL, 35233, USA
| | - Craig P Hersh
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Mark T Dransfield
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - George R Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Merry-Lynn McDonald
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, 701, 19th Street S., LHRB 440, Birmingham, AL, 35233, USA.
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
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15
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Jang SK, Evans L, Fialkowski A, Arnett DK, Ashley-Koch AE, Barnes KC, Becker DM, Bis JC, Blangero J, Bleecker ER, Boorgula MP, Bowden DW, Brody JA, Cade BE, Jenkins BWC, Carson AP, Chavan S, Cupples LA, Custer B, Damrauer SM, David SP, de Andrade M, Dinardo CL, Fingerlin TE, Fornage M, Freedman BI, Garrett ME, Gharib SA, Glahn DC, Haessler J, Heckbert SR, Hokanson JE, Hou L, Hwang SJ, Hyman MC, Judy R, Justice AE, Kaplan RC, Kardia SLR, Kelly S, Kim W, Kooperberg C, Levy D, Lloyd-Jones DM, Loos RJF, Manichaikul AW, Gladwin MT, Martin LW, Nouraie M, Melander O, Meyers DA, Montgomery CG, North KE, Oelsner EC, Palmer ND, Payton M, Peljto AL, Peyser PA, Preuss M, Psaty BM, Qiao D, Rader DJ, Rafaels N, Redline S, Reed RM, Reiner AP, Rich SS, Rotter JI, Schwartz DA, Shadyab AH, Silverman EK, Smith NL, Smith JG, Smith AV, Smith JA, Tang W, Taylor KD, Telen MJ, Vasan RS, Gordeuk VR, Wang Z, Wiggins KL, Yanek LR, Yang IV, Young KA, Young KL, Zhang Y, Liu DJ, Keller MC, Vrieze S. Rare genetic variants explain missing heritability in smoking. Nat Hum Behav 2022; 6:1577-1586. [PMID: 35927319 PMCID: PMC9985486 DOI: 10.1038/s41562-022-01408-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 04/28/2021] [Accepted: 06/10/2022] [Indexed: 12/11/2022]
Abstract
Common genetic variants explain less variation in complex phenotypes than inferred from family-based studies, and there is a debate on the source of this 'missing heritability'. We investigated the contribution of rare genetic variants to tobacco use with whole-genome sequences from up to 26,257 unrelated individuals of European ancestries and 11,743 individuals of African ancestries. Across four smoking traits, single-nucleotide-polymorphism-based heritability ([Formula: see text]) was estimated from 0.13 to 0.28 (s.e., 0.10-0.13) in European ancestries, with 35-74% of it attributable to rare variants with minor allele frequencies between 0.01% and 1%. These heritability estimates are 1.5-4 times higher than past estimates based on common variants alone and accounted for 60% to 100% of our pedigree-based estimates of narrow-sense heritability ([Formula: see text], 0.18-0.34). In the African ancestry samples, [Formula: see text] was estimated from 0.03 to 0.33 (s.e., 0.09-0.14) across the four smoking traits. These results suggest that rare variants are important contributors to the heritability of smoking.
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Affiliation(s)
- Seon-Kyeong Jang
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA
| | - Luke Evans
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Ecology & Evolution, University of Colorado Boulder, Boulder, CO, USA
| | | | - Donna K Arnett
- Dean's Office, University of Kentucky College of Public Health, Lexington, KY, USA
| | | | - Kathleen C Barnes
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Diane M Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | | | - Meher Preethi Boorgula
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E Cade
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brenda W Campbell Jenkins
- Jackson Heart Study Graduate Training and Education Center, Jackson State University School of Public Health, Jackson, MS, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Sameer Chavan
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA
| | - Scott M Damrauer
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Surgery, Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Sean P David
- Department of Family Medicine, Prtizker School of Medicine, University of Chicago, Chicago, IL, USA
- NorthShore University HealthSystem, Evanston, IL, USA
| | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Tasha E Fingerlin
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Center for Genes Environment and Health, National Jewish Health, Denver, CO, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Barry I Freedman
- Section on Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Melanie E Garrett
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Sina A Gharib
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hosptial and Harvard Medical School, Boston, MA, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Shih-Jen Hwang
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthew C Hyman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Renae Judy
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anne E Justice
- Department of Population Health Sciences, Geisinger Health System, Danville, PA, USA
| | - Robert C Kaplan
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Shannon Kelly
- Department of Pediatrics, UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
| | - Wonji Kim
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Framingham Heart Study, Framingham, MA, USA
| | | | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ani W Manichaikul
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Mark T Gladwin
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Mehdi Nouraie
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Olle Melander
- Department of Clinical Sciences, Lund University, Malmö, Sweden
- Department of Internal Medicine, Skåne University Hospital, Malmö, Sweden
| | | | - Courtney G Montgomery
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elizabeth C Oelsner
- Division of General Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Marinelle Payton
- Department of Epidemiology and Biostatistics, Jackson Heart Study Graduate Training and Education Center, Jackson State University School of Public Health, Jackson, MS, USA
| | - Anna L Peljto
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Michael Preuss
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Daniel J Rader
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas Rafaels
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert M Reed
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - David A Schwartz
- Department of Medicine, School of Medicine, University of Colorado Denver, Aurora, CO, USA
- Department of Immunology, School of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Aladdin H Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, USA
| | - J Gustav Smith
- Wallenberg Laboratory/Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University, Gothenburg, Sweden
- Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Albert V Smith
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Weihong Tang
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marilyn J Telen
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Ramachandran S Vasan
- Sections of Preventive Medicine and Epidemiology and Cardiovascular Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Victor R Gordeuk
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Zhe Wang
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ivana V Yang
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kendra A Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yingze Zhang
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Dajiang J Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA
| | - Matthew C Keller
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Scott Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA.
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16
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Litkowski EM, Logue MW, Zhang R, Charest BR, Lange EM, Hokanson JE, Lynch JA, Vujkovic M, Phillips LS, Lange LA, Hauger RL, Raghavan S. A Diabetes Genetic Risk Score Is Associated With All-Cause Dementia and Clinically Diagnosed Vascular Dementia in the Million Veteran Program. Diabetes Care 2022; 45:2544-2552. [PMID: 36041056 PMCID: PMC9679262 DOI: 10.2337/dc22-0105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 07/15/2022] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Diabetes and dementia are diseases of high health care burden worldwide, and studies have shown that diabetes is associated with an increased relative risk of dementia. We set out to examine whether type 2 diabetes-associated genetic variants were associated with dementia and whether they differed by race/ethnicity or clinical dementia diagnosis. RESEARCH DESIGN AND METHODS We evaluated associations of two type 2 diabetes genetic risk scores (GRS and GRS-nonAPOE: a score without rs429358, a variant associated with Alzheimer disease [AD]) with three classifications of clinical dementia diagnoses in the Million Veteran Program (MVP): all-cause dementia, vascular dementia (VaD), and AD. We conducted our analysis stratified by European (EUR), African (AFR), and Hispanic (HIS) races/ethnicities. RESULTS In EUR, we found associations of the GRS with all-cause dementia (odds ratio [OR] 1.06, P = 1.60e-07) and clinically diagnosed VaD (OR 1.12, P = 5.2e-05) but not with clinically diagnosed AD (OR 1.02, P = 0.43). The GRS was not associated with any dementia outcome in AFR or HIS. When testing with GRS-nonAPOE, we found that effect size estimates in EUR increased and P values decreased for all-cause dementia (OR 1.08, P = 2.6e-12), for VaD (OR 1.14, P = 7.2e-07), and for AD (OR 1.06, P = 0.018). For AFR, the association of GRS-nonAPOE and clinically diagnosed VaD (OR 1.15, P = 0.016) was statistically significant. There were no significant findings for HIS. CONCLUSIONS We found evidence suggesting shared genetic pathogenesis of diabetes with all-cause dementia and clinically diagnosed VaD.
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Affiliation(s)
- Elizabeth M. Litkowski
- VA Eastern Colorado Healthcare System, Aurora, CO
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
- Department of Epidemiology, University of Colorado, Aurora, CO
| | - Mark W. Logue
- Behavioral Sciences Division, National Center for PTSD, VA Boston Healthcare System, Boston
- Boston University Schools of Medicine and Public Health, Boston, MA
| | - Rui Zhang
- Behavioral Sciences Division, National Center for PTSD, VA Boston Healthcare System, Boston
| | | | - Ethan M. Lange
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | | | - Julie A. Lynch
- VA Informatics & Computing Infrastructure, VA Salt Lake City Healthcare System, Salt Lake City, UT
- School of Medicine, University of Utah, Salt Lake City, UT
| | - Marijana Vujkovic
- Corporal Michael J. Crescenz Department of Veterans Affairs Medical Center, Philadelphia, PA
- Department of Medicine (M.V.), University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Lawrence S. Phillips
- VA Atlanta Healthcare System, Decatur, GA
- Division of Endocrinology and Metabolism, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Leslie A. Lange
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
- Department of Epidemiology, University of Colorado, Aurora, CO
| | - Richard L. Hauger
- Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, San Diego
- Center for Behavior Genetics of Aging, School of Medicine, University of California, San Diego, La Jolla, CA
| | - Sridharan Raghavan
- VA Eastern Colorado Healthcare System, Aurora, CO
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
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17
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Mathur R, Fang F, Gaddis N, Hancock DB, Cho MH, Hokanson JE, Bierut LJ, Lutz SM, Young K, Smith AV, Silverman EK, Page GP, Johnson EO. GAWMerge expands GWAS sample size and diversity by combining array-based genotyping and whole-genome sequencing. Commun Biol 2022; 5:806. [PMID: 35953715 PMCID: PMC9372058 DOI: 10.1038/s42003-022-03738-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
Genome-wide association studies (GWAS) have made impactful discoveries for complex diseases, often by amassing very large sample sizes. Yet, GWAS of many diseases remain underpowered, especially for non-European ancestries. One cost-effective approach to increase sample size is to combine existing cohorts, which may have limited sample size or be case-only, with public controls, but this approach is limited by the need for a large overlap in variants across genotyping arrays and the scarcity of non-European controls. We developed and validated a protocol, Genotyping Array-WGS Merge (GAWMerge), for combining genotypes from arrays and whole-genome sequencing, ensuring complete variant overlap, and allowing for diverse samples like Trans-Omics for Precision Medicine to be used. Our protocol involves phasing, imputation, and filtering. We illustrated its ability to control technology driven artifacts and type-I error, as well as recover known disease-associated signals across technologies, independent datasets, and ancestries in smoking-related cohorts. GAWMerge enables genetic studies to leverage existing cohorts to validly increase sample size and enhance discovery for understudied traits and ancestries.
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Affiliation(s)
- Ravi Mathur
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Fang Fang
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Nathan Gaddis
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University, St. Louis, MO, USA
| | - Sharon M Lutz
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, MA, USA
| | - Kendra Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Albert V Smith
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Grier P Page
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
- Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA.
- Fellow Program, RTI International, Research Triangle Park, NC, USA.
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18
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Li Y, Dai R, Gwon Y, Rennard SI, Make BJ, Foer D, Strand MJ, Austin E, Young KA, Hokanson JE, Pratte KA, Conway R, Kinney GL. Identifying Individual Medications Affecting Pulmonary Outcomes When Multiple Medications are Present. Clin Epidemiol 2022; 14:731-735. [PMID: 35677475 PMCID: PMC9167843 DOI: 10.2147/clep.s364692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/19/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Yisha Li
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ran Dai
- Department of Biostatistics, School of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yeongjin Gwon
- Department of Biostatistics, School of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Stephen I Rennard
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Barry J Make
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Dinah Foer
- Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Erin Austin
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO, USA
| | - Kendra A Young
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Rebecca Conway
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Gregory L Kinney
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Correspondence: Gregory L Kinney, Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA, Tel +1 303-724-4437, Email
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19
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Young KA, Hokanson JE. Commentary on Chenoweth et al.: Assessing response to interventions for smoking cessation in diverse populations. Addiction 2022; 117:1725-1726. [PMID: 35301772 DOI: 10.1111/add.15865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 02/28/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Kendra A Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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20
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Carlson NE, Horton KW, Hokanson JE, Cleary PA, Jacobs DR, Brunzell JD, Purnell JQ. Weight gain trajectories and obesity rates in intensive and conventional treatments of type 1 diabetes from the DCCT compared with a control population without diabetes. Diabet Med 2022; 39:e14794. [PMID: 35040196 PMCID: PMC9174023 DOI: 10.1111/dme.14794] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 01/13/2022] [Indexed: 11/30/2022]
Abstract
AIM Obesity is a significant health issue for participants with type 1 diabetes undergoing intensive diabetes management. The temporal pattern and factors associated with weight gain after treatment initiation remain poorly understood including how weight gain in participants with and without type I diabetes compare. Our aim was to compare weight gain in those receiving intensive (INT) and conventional (CONV) type 1 diabetes treatment to a population without diabetes. METHODS Participants included men and women of 18 years and older in the Diabetes Control and Complications Trial (DCCT) randomized to INT (n = 562) or CONV (n = 568) and a prospective, observational cohort without diabetes from the Coronary Artery Development in Young Adults (CARDIA, controls) study (n = 2446). Body mass index (BMI) trajectories and obesity prevalence were compared between groups and candidate metabolic and therapeutic moderators investigated. RESULTS Annual weight gain with INT peaked 1.3 years after initiation and was greater than both CONV and controls before and after this peak. Obesity prevalence with INT was lower than controls at baseline, was similar to controls at 2 years and surpassed controls by 5 years. Obesity rates with CONV remained below controls at all time points. Greater annual weight gain in the DCCT was associated with lower haemoglobin A1c , higher insulin dose and family history of type 2 diabetes. CONCLUSIONS Greater weight gain accompanying INT therapy occurs in two stages, leads to similar or greater obesity rates than controls after 2 years and is primarily modified by glucose control and family history, supportive of a therapeutic-genetic influence on weight trajectories.
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Affiliation(s)
- Nichole E Carlson
- Department of Biostatistics and Informatics, University of Colorado-Anschutz Medical Campus, Aurora, CO
| | | | - John E Hokanson
- Department of Epidemiology, University of Colorado-Anschutz Medical Campus, Aurora, CO
| | | | - David R Jacobs
- Division of Epidemiology and Community Health, University of Minnesota
| | - John D Brunzell
- Division of Metabolism, Endocrinology and Nutrition, University of Washington Seattle, WA (deceased)
| | - Jonathan Q Purnell
- Knight Cardiovascular Institute and Division of Endocrinology, Diabetes, and Clinical Nutrition, Department of Medicine, Oregon Health & Science University, Portland, OR
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21
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Wan ES, Hokanson JE, Regan EA, Young KA, Make BJ, DeMeo DL, Mason SE, San Jose Estepar R, Crapo JD, Silverman EK. Significant Spirometric Transitions and Preserved Ratio Impaired Spirometry Among Ever Smokers. Chest 2022; 161:651-661. [PMID: 34592319 PMCID: PMC8941606 DOI: 10.1016/j.chest.2021.09.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/12/2021] [Accepted: 09/15/2021] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Emerging data from longitudinal studies suggest that preserved ratio impaired spirometry (PRISm), defined by proportionate reductions in FEV1 and FVC, is a heterogeneous population with frequent transitions to other lung function categories relative to individuals with normal and obstructive spirometry. Controversy regarding the clinical significance of these transitions exists (eg, whether transitions merely reflect measurement variability or noise). RESEARCH QUESTION Are individuals with PRISm enriched for transitions associated with substantial changes in lung function? STUDY DESIGN AND METHODS Current and former smokers enrolled in the Genetic Epidemiology of COPD (COPDGene) study with spirometry available in phases 1 through 3 (enrollment, 5-year follow-up, and 10-year follow-up) were analyzed. Postbronchodilator lung function categories were as follows: PRISm (FEV1 < 80% predicted with FEV1/FVC ratio ≥ 0.7), Global Initiative for Chronic Obstructive Lung Disease grade 0 (FEV1 ≥ 80% predicted and FEV1/FVC ≥ 0.7), and obstruction (FEV1/FVC < 0.7). Significant transition status was affirmative if a subject belonged to two or more spirometric categories and had > 10% change in FEV1 % predicted and/or FVC % predicted between consecutive visits. Ever-PRISm was present if a subject had PRISm at any visit. Logistic regression examined the association between significant transitions and ever-PRISm status, adjusted for age, sex, race, FEV1 % predicted, current smoking, pack-years, BMI, and ever-positive bronchodilator response. RESULTS Among subjects with complete data (N = 1,775) over 10.1 ± 0.4 years of follow-up, the prevalence of PRISm remained consistent (10.4%-11.3%) between phases 1 through 3, but nearly one-half of subjects with PRISm transitioned into or out of PRISm at each visit. Among all subjects, 19.7% had a significant transition; ever-PRISm was a significant predictor of significant transitions (unadjusted OR, 10.3; 95% CI, 7.9-13.5; adjusted OR, 14.9; 95% CI, 10.9-20.7). Results were similar with additional adjustment for radiographic emphysema and gas trapping, when lower limit of normal criteria were used to define lung function categories, and when FEV1 alone (regardless of change in FVC % predicted) was used to define significant transitions. INTERPRETATION PRISm is an unstable group, with frequent significant transitions to both obstruction and normal spirometry over time. CLINICAL TRIAL REGISTRATION ClinicalTrials.gov; No.: NCT000608764; URL: www. CLINICALTRIALS gov.
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Affiliation(s)
- Emily S. Wan
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA,Pulmonary & Critical Care Section, VA Boston Healthcare System, Boston, MA,CORRESPONDENCE TO: Emily S. Wan, MD, MPH
| | - John E. Hokanson
- University of Colorado, Denver, CO,Department of Epidemiology, Colorado School of Public Health, University of Colorado, Denver, CO
| | - Elizabeth A. Regan
- Department of Epidemiology, Colorado School of Public Health, University of Colorado, Denver, CO,National Jewish Health, Denver, CO
| | - Kendra A. Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado, Denver, CO
| | | | - Dawn L. DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Stefanie E. Mason
- Division of Pulmonary and Critical Care, Brigham and Women's Hospital, Boston, MA
| | | | | | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA
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22
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Mason SE, Moreta-Martinez R, Labaki WW, Strand MJ, Regan EA, Bon J, San Jose Estepar R, Casaburi R, McDonald ML, Rossiter HB, Make B, Dransfield MT, Han MK, Young K, Curtis JL, Stringer K, Kinney G, Hokanson JE, San Jose Estepar R, Washko GR. Longitudinal association between muscle loss and mortality in ever-smokers. Chest 2021; 161:960-970. [PMID: 34785234 DOI: 10.1016/j.chest.2021.10.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/25/2021] [Accepted: 10/23/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Body composition measures, specifically low weight or reduced muscle mass, are associated with mortality in chronic obstructive pulmonary disease (COPD), but the effect of longitudinal body composition changes is undefined. RESEARCH QUESTION Is the longitudinal loss of fat-free mass (FFM) associated with increased mortality including in those with initially normal or elevated body composition metrics? STUDY DESIGN AND METHODS Participants with complete data for at least one visit in the COPDGene (n=9,268) and ECLIPSE studies (1,760) were included and followed for 12 and 8 years, respectively. Pectoralis muscle area (PMA) was derived from thoracic CT scans and used as a proxy for FFM. A longitudinal mixed sub-model for PMA and a Cox proportional hazards sub-model for survival were fitted on a joint distribution using a shared random intercept parameter and Markov chain Monte Carlo parameter estimation. RESULTS Both cohorts demonstrated a left shifted distribution of baseline FFM, not reflected in BMI, and an increase in all-cause mortality risk associated with longitudinal loss of PMA. For each one cm2 PMA loss, mortality increased 3.1% (95% CI 2.4, 3.7, p<0.001) in COPDGene, and 2.4% (95% CI 0.9, 4.0, p<0.001) in ECLIPSE. Increased mortality risk was independent of enrollment values for BMI and disease severity (BODE index quartiles) and was significant even in participants with initially greater than average PMA. INTERPRETATION Longitudinal loss of PMA is associated with increased all-cause mortality, regardless of BMI or initial muscle mass. Consideration of novel screening tests and further research into mechanisms contributing to muscle decline may improve risk stratification and identify novel therapeutic targets in ever-smokers.
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Affiliation(s)
- Stefanie E Mason
- Department of Medicine, Division of Pulmonary and Critical Care, Brigham and Women's Hospital, Boston MA.
| | | | - Wassim W Labaki
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor MI
| | - Matthew J Strand
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver CO
| | - Elizabeth A Regan
- Department of Medicine, Division of Rheumatology, National Jewish Health, Denver CO
| | - Jessica Bon
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Pittsburgh PA; VA Pittsburgh Healthcare System, Pittsburgh, PA
| | | | - Richard Casaburi
- Rehabilitation Clinical Trials Center, Division of Pulmonary and Critical Care Physiology and Medicine, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance CA
| | - Merry-Lynn McDonald
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care, University of Alabama at Birmingham, Birmingham AL
| | - Harry B Rossiter
- Rehabilitation Clinical Trials Center, Division of Pulmonary and Critical Care Physiology and Medicine, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance CA
| | - Barry Make
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, National Jewish Health, Denver CO
| | - Mark T Dransfield
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care, University of Alabama at Birmingham, Birmingham AL
| | - MeiLan K Han
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor MI
| | - Kendra Young
- Department of Epidemiology, Colorado School of Public Health, Aurora CO
| | - Jeffrey L Curtis
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor MI; Medical Service, VA Ann Arbor Healthcare System, Ann Arbor, MI
| | - Kathleen Stringer
- Department of Clinical Sciences, University of Michigan College of Pharmacy, Ann Arbor, MI
| | - Greg Kinney
- Department of Epidemiology, Colorado School of Public Health, Aurora CO
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, Aurora CO
| | | | - George R Washko
- Department of Medicine, Division of Pulmonary and Critical Care, Brigham and Women's Hospital, Boston MA
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23
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Fortis S, Wan ES, Kunisaki K, Eyck PT, Ballas ZK, Bowler RP, Crapo JD, Hokanson JE, Wendt C, Silverman EK, Comellas AP. Increased mortality associated with frequent exacerbations in COPD patients with mild-to-moderate lung function impairment, and smokers with normal spirometry. Respiratory Medicine: X 2021; 3. [PMID: 35911870 PMCID: PMC9333066 DOI: 10.1016/j.yrmex.2020.100025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Indexed: 11/17/2022] Open
Abstract
Background: Methods: Results: Conclusions:
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Affiliation(s)
- Spyridon Fortis
- Center for Access & Delivery Research & Evaluation (CADRE), Iowa City VA Health Care System, Iowa City, IA, USA
- Division of Pulmonary, Critical Care and Occupational Medicine, University of Iowa Hospital and Clinics, Iowa City, IA, USA
- Corresponding author. UIHC – Internal Medicine, 200 Hawkins Drive – C33 GH, Iowa City, IA, 52242, USA. (S. Fortis)
| | - Emily S. Wan
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- VA Boston Healthcare System, Jamaica Plain, MA, USA
| | - Ken Kunisaki
- Minneapolis Veterans Affairs Health Care System, Minneapolis, MN, USA
- University of Minnesota, Minneapolis, MN, USA
| | - Patrick Tel Eyck
- Biostatistics and Research Design, Institute for Clinical and Translational Science, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Zuhair K. Ballas
- Division of Immunology, Department of Internal Medicine, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | | | - James D. Crapo
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - John E. Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Chris Wendt
- Minneapolis Veterans Affairs Health Care System, Minneapolis, MN, USA
- University of Minnesota, Minneapolis, MN, USA
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Alejandro P. Comellas
- Division of Pulmonary, Critical Care and Occupational Medicine, University of Iowa Hospital and Clinics, Iowa City, IA, USA
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24
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Pistenmaa CL, Nardelli P, Ash SY, Come CE, Diaz AA, Rahaghi FN, Barr RG, Young KA, Kinney GL, Simmons JP, Wade RC, Wells JM, Hokanson JE, Washko GR, San José Estépar R. Pulmonary Arterial Pruning and Longitudinal Change in Percent Emphysema and Lung Function: The Genetic Epidemiology of COPD Study. Chest 2021; 160:470-480. [PMID: 33607083 PMCID: PMC8411454 DOI: 10.1016/j.chest.2021.01.084] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 09/14/2020] [Revised: 12/28/2020] [Accepted: 01/23/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Pulmonary endothelial damage has been shown to precede the development of emphysema in animals, and vascular changes in humans have been observed in COPD and emphysema. RESEARCH QUESTION Is intraparenchymal vascular pruning associated with longitudinal progression of emphysema on CT imaging or decline in lung function over 5 years? STUDY DESIGN AND METHODS The Genetic Epidemiology of COPD Study enrolled ever smokers with and without COPD from 2008 through 2011. The percentage of emphysema-like lung, or "percent emphysema," was assessed at baseline and after 5 years on noncontrast CT imaging as the percentage of lung voxels < -950 Hounsfield units. An automated CT imaging-based tool assessed and classified intrapulmonary arteries and veins. Spirometry measures are postbronchodilator. Pulmonary arterial pruning was defined as a lower ratio of small artery volume (< 5 mm2 cross-sectional area) to total lung artery volume. Mixed linear models included demographics, anthropomorphics, smoking, and COPD, with emphysema models also adjusting for CT imaging scanner and lung function models adjusting for clinical center and baseline percent emphysema. RESULTS At baseline, the 4,227 participants were 60 ± 9 years of age, 50% were women, 28% were Black, 47% were current smokers, and 41% had COPD. Median percent emphysema was 2.1 (interquartile range, 0.6-6.3) and progressed 0.24 percentage points/y (95% CI, 0.22-0.26 percentage points/y) over 5.6 years. Mean FEV1 to FVC ratio was 68.5 ± 14.2% and declined 0.26%/y (95% CI, -0.30 to -0.23%/y). Greater pulmonary arterial pruning was associated with more rapid progression of percent emphysema (0.11 percentage points/y per 1-SD increase in arterial pruning; 95% CI, 0.09-0.16 percentage points/y), including after adjusting for baseline percent emphysema and FEV1. Arterial pruning also was associated with a faster decline in FEV1 to FVC ratio (-0.04%/y per 1-SD increase in arterial pruning; 95% CI, -0.008 to -0.001%/y). INTERPRETATION Pulmonary arterial pruning was associated with faster progression of percent emphysema and more rapid decline in FEV1 to FVC ratio over 5 years in ever smokers, suggesting that pulmonary vascular differences may be relevant in disease progression. TRIAL REGISTRY ClinicalTrials.gov; No.: NCT00608764; URL: www.clinicaltrials.gov.
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Affiliation(s)
| | - P Nardelli
- Department of Radiology, Brigham and Women's Hospital, Boston, MA
| | - S Y Ash
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - C E Come
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - A A Diaz
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - F N Rahaghi
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - R G Barr
- Departments of Medicine and Epidemiology, Columbia University, New York, NY
| | - K A Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado, Denver, CO
| | - G L Kinney
- Department of Epidemiology, Colorado School of Public Health, University of Colorado, Denver, CO
| | - J P Simmons
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - R C Wade
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - J M Wells
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - J E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado, Denver, CO
| | - G R Washko
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
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25
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Lutz SM, Wu AC, Hokanson JE, Vansteelandt S, Lange C. Caution against examining the role of reverse causality in Mendelian Randomization. Genet Epidemiol 2021; 45:445-454. [PMID: 34008876 DOI: 10.1002/gepi.22385] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 03/13/2021] [Accepted: 04/13/2021] [Indexed: 12/18/2022]
Abstract
Recently, Mendelian Randomization (MR) has gained in popularity as a concept to assess the causal relationship between phenotypes in genetic association studies. An extension of standard MR methodology, the MR Steiger approach, has recently been developed to infer the causal direction between two phenotypes in prospective studies. Through simulation studies, we examined and quantified the ability of the MR Steiger approach to determine the causal direction between two phenotypes (i.e., effect direction). Through simulation studies, our results show that the MR Steiger approach may fail to correctly identify the direction of causality. This is true, especially in the presence of pleiotropy. We also applied the MR Steiger method to the COPDGene study, a case-control study of chronic obstructive pulmonary disease (COPD) in current and former smokers, to examine the role of smoking on lung function. We have created an R package on Github called reverseDirection which runs simulations for user-specified scenarios to examine when the MR Steiger approach can correctly determine the causal direction between two phenotypes in any user specified scenario. In summary, our results emphasize the importance of caution when the MR Steiger approach is used in to infer the direction of causality.
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Affiliation(s)
- Sharon M Lutz
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Ann Chen Wu
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA
| | - John E Hokanson
- Department of Epidemiology, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
| | - Stijn Vansteelandt
- Department of Applied Mathematics, Computer Science, and Statistics, Ghent University, Ghent, Belgium.,Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, UK
| | - Christoph Lange
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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26
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Mason SE, Moreta-Martinez R, Labaki WW, Strand M, Baraghoshi D, Regan EA, Bon J, San Jose Estepar R, Casaburi R, McDonald MLN, Rossiter H, Make BJ, Dransfield MT, Han MK, Young KA, Kinney G, Hokanson JE, San Jose Estepar R, Washko GR. Respiratory exacerbations are associated with muscle loss in current and former smokers. Thorax 2021; 76:554-560. [PMID: 33574123 DOI: 10.1136/thoraxjnl-2020-215999] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/30/2020] [Accepted: 12/21/2020] [Indexed: 01/07/2023]
Abstract
OBJECTIVES Muscle wasting is a recognised extra-pulmonary complication in chronic obstructive pulmonary disease and has been associated with increased risk of death. Acute respiratory exacerbations are associated with reduction of muscle function, but there is a paucity of data on their long-term effect. This study explores the relationship between acute respiratory exacerbations and long-term muscle loss using serial measurements of CT derived pectoralis muscle area (PMA). DESIGN AND SETTING Participants were included from two prospective, longitudinal, observational, multicentre cohorts of ever-smokers with at least 10 pack-year history. PARTICIPANTS The primary analysis included 1332 (of 2501) participants from Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE) and 4384 (of 10 198) participants from Genetic Epidemiology of COPD (COPDGene) who had complete data from their baseline and follow-up visits. INTERVENTIONS PMA was measured on chest CT scans at two timepoints. Self-reported exacerbation data were collected from participants in both studies through the use of periodic longitudinal surveys. MAIN OUTCOME MEASURES Age-related and excess muscle loss over time. RESULTS Age, sex, race and body mass index were associated with baseline PMA. Participants experienced age-related decline at the upper end of reported normal ranges. In ECLIPSE, the exacerbation rate over time was associated with an excess muscle area loss of 1.3% (95% CI 0.6 to 1.9, p<0.001) over 3 years and in COPDGene with an excess muscle area loss of 2.1% (95% CI 1.2 to 2.8, p<0.001) over 5 years. Excess muscle area decline was absent in 273 individuals who participated in pulmonary rehabilitation. CONCLUSIONS Exacerbations are associated with accelerated skeletal muscle loss. Each annual exacerbation was associated with the equivalent of 6 months of age-expected decline in muscle mass. Ameliorating exacerbation-associated muscle loss represents an important therapeutic target.
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Affiliation(s)
- Stefanie Elizabeth Mason
- Division of Pulmonary and Critical Care, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | - Wassim W Labaki
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Matthew Strand
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, Colorado, USA
| | - David Baraghoshi
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, Colorado, USA
| | - Elizabeth A Regan
- Division of Rheumatology, National Jewish Health, Denver, Colorado, USA
| | - Jessica Bon
- Division of Pulmonary, Allergy and Critical Care, UPMC, Pittsburgh, Pennsylvania, USA
| | | | - Richard Casaburi
- Division of Respiratory and Critical Care Physiology and Medicine, Los Angeles Biomedical Research Institute, Torrance, California, USA
| | - Merry-Lynn N McDonald
- Division of Pulmonary, Allergy, and Critical Care, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Harry Rossiter
- Division of Respiratory and Critical Care Physiology and Medicine, Los Angeles Biomedical Research Institute, Torrance, California, USA
| | - Barry J Make
- Division of Pulmonary, Critical Care, and Sleep Medicine, National Jewish Health, Denver, Colorado, USA
| | - Mark T Dransfield
- Division of Pulmonary, Allergy, and Critical Care, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - MeiLan K Han
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Kendra A Young
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA
| | - Greg Kinney
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, USA
| | | | - George R Washko
- Division of Pulmonary and Critical Care, Brigham and Women's Hospital, Boston, Massachusetts, USA
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27
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Quach BC, Bray MJ, Gaddis NC, Liu M, Palviainen T, Minica CC, Zellers S, Sherva R, Aliev F, Nothnagel M, Young KA, Marks JA, Young H, Carnes MU, Guo Y, Waldrop A, Sey NYA, Landi MT, McNeil DW, Drichel D, Farrer LA, Markunas CA, Vink JM, Hottenga JJ, Iacono WG, Kranzler HR, Saccone NL, Neale MC, Madden P, Rietschel M, Marazita ML, McGue M, Won H, Winterer G, Grucza R, Dick DM, Gelernter J, Caporaso NE, Baker TB, Boomsma DI, Kaprio J, Hokanson JE, Vrieze S, Bierut LJ, Johnson EO, Hancock DB. Expanding the genetic architecture of nicotine dependence and its shared genetics with multiple traits. Nat Commun 2020; 11:5562. [PMID: 33144568 PMCID: PMC7642344 DOI: 10.1038/s41467-020-19265-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [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: 01/21/2020] [Accepted: 09/24/2020] [Indexed: 12/31/2022] Open
Abstract
Cigarette smoking is the leading cause of preventable morbidity and mortality. Genetic variation contributes to initiation, regular smoking, nicotine dependence, and cessation. We present a Fagerström Test for Nicotine Dependence (FTND)-based genome-wide association study in 58,000 European or African ancestry smokers. We observe five genome-wide significant loci, including previously unreported loci MAGI2/GNAI1 (rs2714700) and TENM2 (rs1862416), and extend loci reported for other smoking traits to nicotine dependence. Using the heaviness of smoking index from UK Biobank (N = 33,791), rs2714700 is consistently associated; rs1862416 is not associated, likely reflecting nicotine dependence features not captured by the heaviness of smoking index. Both variants influence nearby gene expression (rs2714700/MAGI2-AS3 in hippocampus; rs1862416/TENM2 in lung), and expression of genes spanning nicotine dependence-associated variants is enriched in cerebellum. Nicotine dependence (SNP-based heritability = 8.6%) is genetically correlated with 18 other smoking traits (rg = 0.40-1.09) and co-morbidities. Our results highlight nicotine dependence-specific loci, emphasizing the FTND as a composite phenotype that expands genetic knowledge of smoking.
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Affiliation(s)
- Bryan C Quach
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Michael J Bray
- Department of Psychiatry, Washington University, St. Louis, MO, 63130, USA
| | - Nathan C Gaddis
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Mengzhen Liu
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Teemu Palviainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00290, Helsinki, Finland
| | - Camelia C Minica
- Department of Biological Psychology, Vrije Universiteit, 1081 BT, Amsterdam, The Netherlands
| | - Stephanie Zellers
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Richard Sherva
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, 02118, USA
| | - Fazil Aliev
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Faculty of Business, Karabuk University, 78050, Kılavuzlar/Karabük Merkez/Karabük, Turkey
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, 50931, Köln, Germany
- University Hospital Cologne, 50931, Köln, Germany
| | - Kendra A Young
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Jesse A Marks
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Hannah Young
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Megan U Carnes
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Yuelong Guo
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
- GeneCentric Therapeutics, Research Triangle Park, NC, 27709, USA
| | - Alex Waldrop
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Nancy Y A Sey
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Maria T Landi
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, 20892, USA
| | - Daniel W McNeil
- Department of Psychology, West Virginia University, Morgantown, WV, 26505, USA
- Department of Dental Practice and Rural Health, West Virginia University, Morgantown, WV, 26505, USA
| | - Dmitriy Drichel
- Cologne Center for Genomics, University of Cologne, 50931, Köln, Germany
- University Hospital Cologne, 50931, Köln, Germany
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Ophthalmology, Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, 02118, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Christina A Markunas
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
| | - Jacqueline M Vink
- Behavioural Science Institute, Radboud University, 6500 HE, Nijmegen, The Netherlands
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit, 1081 BT, Amsterdam, The Netherlands
| | - William G Iacono
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Henry R Kranzler
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- VISN 4 MIRECC, Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
| | - Nancy L Saccone
- Department of Genetics, Washington University, St. Louis, MO, 63130, USA
- Division of Biostatistics, Washington University, St. Louis, MO, 63130, USA
| | - Michael C Neale
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Pamela Madden
- Department of Psychiatry, Washington University, St. Louis, MO, 63130, USA
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, 68159, Mannheim, Germany
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Matthew McGue
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Georg Winterer
- Experimental & Clinical Research Center, Department of Anesthesiology and Operative Intensive Care Medicine, Charité - University Medicine Berlin, 10117, Berlin, Germany
| | - Richard Grucza
- Departments of Family and Community Medicine and Health and Clinical Outcomes Research, Saint Louis University, St. Louis, MO, 63130, USA
| | - Danielle M Dick
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- College Behavioral and Emotional Health Institute, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, 06511, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06511, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06511, USA
- Department of Psychiatry, VA CT Healthcare Center, West Haven, CT, 06511, USA
| | - Neil E Caporaso
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, 20892, USA
| | - Timothy B Baker
- Center for Tobacco Research and Intervention, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53726, USA
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit, 1081 BT, Amsterdam, The Netherlands
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00290, Helsinki, Finland
- Department of Public Health, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Scott Vrieze
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University, St. Louis, MO, 63130, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA
- Fellow Program, RTI International, Research Triangle Park, NC, 27709, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, 27709, USA.
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28
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Li Y, Ragland M, Austin E, Young K, Pratte K, Hokanson JE, Beaty TH, Regan EA, Rennard SI, Wern C, Jacobs MR, Tal-Singer R, Make BJ, Kinney GL. Co-Morbidity Patterns Identified Using Latent Class Analysis of Medications Predict All-Cause Mortality Independent of Other Known Risk Factors: The COPDGene ® Study. Clin Epidemiol 2020; 12:1171-1181. [PMID: 33149694 PMCID: PMC7602898 DOI: 10.2147/clep.s279075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/06/2020] [Indexed: 01/21/2023] Open
Abstract
PURPOSE Medication patterns include all medications in an individual's clinical profile. We aimed to identify chronic co-morbidity treatment patterns through medication use among COPDGene participants and determine whether these patterns were associated with mortality, acute exacerbations of chronic obstructive pulmonary disease (AECOPD) and quality of life. MATERIALS AND METHODS Participants analyzed here completed Phase 1 (P1) and/or Phase 2 (P2) of COPDGene. Latent class analysis (LCA) was used to identify medication patterns and assign individuals into unobserved LCA classes. Mortality, AECOPD, and the St. George's Respiratory Questionnaire (SGRQ) health status were compared in different LCA classes through survival analysis, logistic regression, and Kruskal-Wallis test, respectively. RESULTS LCA identified 8 medication patterns from 32 classes of chronic comorbid medications. A total of 8110 out of 10,127 participants with complete covariate information were included. Survival analysis adjusted for covariates showed, compared to a low medication use class, mortality was highest in participants with hypertension+diabetes+statin+antiplatelet medication group. Participants in hypertension+SSRI+statin medication group had the highest odds of AECOPD and the highest SGRQ score at both P1 and P2. CONCLUSION Medication pattern can serve as a good indicator of an individual's comorbidities profile and improves models predicting clinical outcomes.
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Affiliation(s)
- Yisha Li
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Margaret Ragland
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Erin Austin
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO, USA
| | - Kendra Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Terri H Beaty
- Bloomberg School of Public Health, University of John Hopkins, Baltimore, MD, USA
| | | | - Stephen I Rennard
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NB, USA
| | - Christina Wern
- Department of Clinical Pharmacy, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | | | | | | - Gregory L Kinney
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - On Behalf of theCOPDGene investigators
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO, USA
- National Jewish Health, Denver, CO, USA
- Bloomberg School of Public Health, University of John Hopkins, Baltimore, MD, USA
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NB, USA
- Department of Clinical Pharmacy, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- School of Pharmacy, Temple University, PA, Pennsylvania, USA
- COPD Foundation, Washington, D.C., USA
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29
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Kim W, Prokopenko D, Sakornsakolpat P, Hobbs BD, Lutz SM, Hokanson JE, Wain LV, Melbourne CA, Shrine N, Tobin MD, Silverman EK, Cho MH, Beaty TH. Genome-Wide Gene-by-Smoking Interaction Study of Chronic Obstructive Pulmonary Disease. Am J Epidemiol 2020; 190:875-885. [PMID: 33106845 PMCID: PMC8096488 DOI: 10.1093/aje/kwaa227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 09/28/2020] [Accepted: 10/13/2020] [Indexed: 01/20/2023] Open
Abstract
Risk of chronic obstructive pulmonary disease (COPD) is determined by both cigarette smoking and genetic susceptibility, but little is known about gene-by-smoking interactions. We performed a genome-wide association analysis of 179,689 controls and 21,077 COPD cases from UK Biobank subjects of European ancestry recruited from 2006 to 2010, considering genetic main effects and gene-by-smoking interaction effects simultaneously (2-degrees-of-freedom (df) test) as well as interaction effects alone (1-df interaction test). We sought to replicate significant results in COPDGene (United States, 2008-2010) and SpiroMeta Consortium (multiple countries, 1947-2015) data. We considered 2 smoking variables: 1) ever/never and 2) current/noncurrent. In the 1-df test, we identified 1 genome-wide significant locus on 15q25.1 (cholinergic receptor nicotinic β4 subunit, or CHRNB4) for ever- and current smoking and identified PI*Z allele (rs28929474) of serpin family A member 1 (SERPINA1) for ever-smoking and 3q26.2 (MDS1 and EVI1 complex locus, or MECOM) for current smoking in an analysis of previously reported COPD loci. In the 2-df test, most of the significant signals were also significant for genetic marginal effects, aside from 16q22.1 (sphingomyelin phosphodiesterase 3, or SMPD3) and 19q13.2 (Egl-9 family hypoxia inducible factor 2, or EGLN2). The significant effects at 15q25.1 and 19q13.2 loci, both previously described in prior genome-wide association studies of COPD or smoking, were replicated in COPDGene and SpiroMeta. We identified interaction effects at previously reported COPD loci; however, we failed to identify novel susceptibility loci.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Terri H Beaty
- Correspondence to Dr. Terri H. Beaty, Department of Epidemiology, Johns Hopkins School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 (e-mail: )
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30
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Chen J, Loukola A, Gillespie NA, Peterson R, Jia P, Riley B, Maes H, Dick DM, Kendler KS, Damaj MI, Miles MF, Zhao Z, Li MD, Vink JM, Minica CC, Willemsen G, Boomsma DI, Qaiser B, Madden PAF, Korhonen T, Jousilahti P, Hällfors J, Gelernter J, Kranzler HR, Sherva R, Farrer L, Maher B, Vanyukov M, Taylor M, Ware JJ, Munafò MR, Lutz SM, Hokanson JE, Gu F, Landi MT, Caporaso NE, Hancock DB, Gaddis NC, Baker TB, Bierut LJ, Johnson EO, Chenoweth M, Lerman C, Tyndale R, Kaprio J, Chen X. Genome-Wide Meta-Analyses of FTND and TTFC Phenotypes. Nicotine Tob Res 2020; 22:900-909. [PMID: 31294817 DOI: 10.1093/ntr/ntz099] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/14/2018] [Indexed: 12/19/2022]
Abstract
INTRODUCTION FTND (Fagerstrӧm test for nicotine dependence) and TTFC (time to smoke first cigarette in the morning) are common measures of nicotine dependence (ND). However, genome-wide meta-analysis for these phenotypes has not been reported. METHODS Genome-wide meta-analyses for FTND (N = 19,431) and TTFC (N = 18,567) phenotypes were conducted for adult smokers of European ancestry from 14 independent cohorts. RESULTS We found that SORBS2 on 4q35 (p = 4.05 × 10-8), BG182718 on 11q22 (p = 1.02 × 10-8), and AA333164 on 14q21 (p = 4.11 × 10-9) were associated with TTFC phenotype. We attempted replication of leading candidates with independent samples (FTND, N = 7010 and TTFC, N = 10 061), however, due to limited power of the replication samples, the replication of these new loci did not reach significance. In gene-based analyses, COPB2 was found associated with FTND phenotype, and TFCP2L1, RELN, and INO80C were associated with TTFC phenotype. In pathway and network analyses, we found that the interconnected interactions among the endocytosis, regulation of actin cytoskeleton, axon guidance, MAPK signaling, and chemokine signaling pathways were involved in ND. CONCLUSIONS Our analyses identified several promising candidates for both FTND and TTFC phenotypes, and further verification of these candidates was necessary. Candidates supported by both FTND and TTFC (CHRNA4, THSD7B, RBFOX1, and ZNF804A) were associated with addiction to alcohol, cocaine, and heroin, and were associated with autism and schizophrenia. We also identified novel pathways involved in cigarette smoking. The pathway interactions highlighted the importance of receptor recycling and internalization in ND. IMPLICATIONS Understanding the genetic architecture of cigarette smoking and ND is critical to develop effective prevention and treatment. Our study identified novel candidates and biological pathways involved in FTND and TTFC phenotypes, and this will facilitate further investigation of these candidates and pathways.
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Affiliation(s)
- Jingchun Chen
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV
| | - Anu Loukola
- Department of Public Health, University of Helsinki, Helsinki, FI, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Nathan A Gillespie
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - Roseann Peterson
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - Peilin Jia
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX
| | - Brien Riley
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - Hermine Maes
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - Daniella M Dick
- Department of Psychology, Virginia Commonwealth University, Richmond, VA
| | - Kenneth S Kendler
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
| | - M Imad Damaj
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA
| | - Michael F Miles
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA
| | - Zhongming Zhao
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX
| | - Ming D Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jacqueline M Vink
- Netherlands Twin Register, Department of Biological Psychology, VU University, the Netherlands.,Behavioural Science Institute, Radboud University, Nijmegen, the Netherlands
| | - Camelia C Minica
- Netherlands Twin Register, Department of Biological Psychology, VU University, the Netherlands.,Neuroscience Campus Amsterdam, the Netherlands.,EMGO+ Institute for Health and Care Research, VU Medical Center, Amsterdam, the Netherlands
| | - Gonneke Willemsen
- Netherlands Twin Register, Department of Biological Psychology, VU University, the Netherlands.,Neuroscience Campus Amsterdam, the Netherlands.,EMGO+ Institute for Health and Care Research, VU Medical Center, Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Netherlands Twin Register, Department of Biological Psychology, VU University, the Netherlands.,Neuroscience Campus Amsterdam, the Netherlands.,EMGO+ Institute for Health and Care Research, VU Medical Center, Amsterdam, the Netherlands
| | - Beenish Qaiser
- Department of Public Health, University of Helsinki, Helsinki, FI, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - Tellervo Korhonen
- Department of Public Health, University of Helsinki, Helsinki, FI, Finland.,Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Finland
| | | | - Jenni Hällfors
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Joel Gelernter
- Department of Psychiatry, Yale University, New Haven, CT
| | - Henry R Kranzler
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA
| | - Richard Sherva
- Section of Biomedical Genetics, Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Lindsay Farrer
- Section of Biomedical Genetics, Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Brion Maher
- Department of Mental Health, Johns Hopkins University, Baltimore, MD
| | - Michael Vanyukov
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Michelle Taylor
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, BS, UK
| | - Jenifer J Ware
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, BS, UK
| | - Marcus R Munafò
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, Bristol, BS, UK
| | - Sharon M Lutz
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - John E Hokanson
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Fangyi Gu
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD
| | - Maria T Landi
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD
| | - Neil E Caporaso
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD
| | - Dana B Hancock
- Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC
| | - Nathan C Gaddis
- Research Computing Division, RTI International, Research Triangle Park, NC
| | - Timothy B Baker
- Center for Tobacco Research and Intervention, University of Wisconsin, Madison, WI
| | - Laura J Bierut
- Department of Psychiatry, Washington University, St. Louis, MO
| | - Eric O Johnson
- Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC.,Fellow Program, RTI International, Research Triangle Park, NC
| | - Meghan Chenoweth
- Centre for Addiction and Mental Health, and Departments of Pharmacology and Toxicology, and Psychiatry, University of Toronto, Toronto, Canada
| | - Caryn Lerman
- Center for Interdisciplinary Research on Nicotine Addiction, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA
| | - Rachel Tyndale
- Centre for Addiction and Mental Health, and Departments of Pharmacology and Toxicology, and Psychiatry, University of Toronto, Toronto, Canada
| | - Jaakko Kaprio
- Department of Public Health, University of Helsinki, Helsinki, FI, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Xiangning Chen
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV.,Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA.,Department of Psychology, University of Nevada Las Vegas, Las Vegas, NV
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31
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Bray MJ, Chen LS, Fox L, Hancock DB, Culverhouse RC, Hartz SM, Johnson EO, Liu M, McKay JD, Saccone NL, Hokanson JE, Vrieze SI, Tyndale RF, Baker TB, Bierut LJ. Dissecting the genetic overlap of smoking behaviors, lung cancer, and chronic obstructive pulmonary disease: A focus on nicotinic receptors and nicotine metabolizing enzyme. Genet Epidemiol 2020; 44:748-758. [PMID: 32803792 PMCID: PMC7793026 DOI: 10.1002/gepi.22331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 02/21/2020] [Revised: 05/14/2020] [Accepted: 06/18/2020] [Indexed: 12/17/2022]
Abstract
Smoking is a major contributor to lung cancer and chronic obstructive pulmonary disease (COPD). Two of the strongest genetic associations of smoking-related phenotypes are the chromosomal regions 15q25.1, encompassing the nicotinic acetylcholine receptor subunit genes CHRNA5-CHRNA3-CHRNB4, and 19q13.2, encompassing the nicotine metabolizing gene CYP2A6. In this study, we examined genetic relations between cigarettes smoked per day, smoking cessation, lung cancer, and COPD. Data consisted of genome-wide association study summary results. Genetic correlations were estimated using linkage disequilibrium score regression software. For each pair of outcomes, z-score-z-score (ZZ) plots were generated. Overall, heavier smoking and decreased smoking cessation showed positive genetic associations with increased lung cancer and COPD risk. The chromosomal region 19q13.2, however, showed a different correlational pattern. For example, the effect allele-C of the sentinel SNP (rs56113850) within CYP2A6 was associated with an increased risk of heavier smoking (z-score = 19.2; p = 1.10 × 10-81 ), lung cancer (z-score = 8.91; p = 5.02 × 10-19 ), and COPD (z-score = 4.04; p = 5.40 × 10-5 ). Surprisingly, this allele-C (rs56113850) was associated with increased smoking cessation (z-score = -8.17; p = 2.52 × 10-26 ). This inverse relationship highlights the need for additional investigation to determine how CYP2A6 variation could increase smoking cessation while also increasing the risk of lung cancer and COPD likely through increased cigarettes smoked per day.
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Affiliation(s)
- Michael J. Bray
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
| | - Li-Shiun Chen
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
- The Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | - Louis Fox
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
| | - Dana B. Hancock
- Center for Omics Discovery and Epidemiology, Behavioral Health Research Division, RTI International, Research Triangle Park, NC
| | - Robert C. Culverhouse
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO
| | - Sarah M. Hartz
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
| | - Eric O. Johnson
- Center for Omics Discovery and Epidemiology, Behavioral Health Research Division, RTI International, Research Triangle Park, NC
- Fellow Program, RTI International, Research Triangle Park, NC
| | - Mengzhen Liu
- Department of Psychology, University of Minnesota, Minnesota, MN
| | - James D. McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Nancy L. Saccone
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - John E. Hokanson
- Department of Epidemiology, University of Colorado, Denver, Aurora, CO
| | - Scott I. Vrieze
- Department of Psychology, University of Minnesota, Minnesota, MN
| | - Rachel F. Tyndale
- Centre for Addiction and Mental Health and Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Timothy B. Baker
- Center for Tobacco Research and Intervention, University of Wisconsin, School of Medicine and Public Health, Madison, WI
| | - Laura J. Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
- The Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
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32
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Strand M, Austin E, Moll M, Pratte KA, Regan EA, Hayden LP, Bhatt SP, Boriek AM, Casaburi R, Silverman EK, Fortis S, Ruczinski I, Koegler H, Rossiter HB, Occhipinti M, Hanania NA, Gebrekristos HT, Lynch DA, Kunisaki KM, Young KA, Sieren JC, Ragland M, Hokanson JE, Lutz SM, Make BJ, Kinney GL, Cho MH, Pistolesi M, DeMeo DL, Sciurba FC, Comellas AP, Diaz AA, Barjaktarevic I, Bowler RP, Kanner RE, Peters SP, Ortega VE, Dransfield MT, Crapo JD. A Risk Prediction Model for Mortality Among Smokers in the COPDGene® Study. Chronic Obstr Pulm Dis 2020; 7:346-361. [PMID: 32877963 PMCID: PMC7883903 DOI: 10.15326/jcopdf.7.4.2020.0146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/15/2020] [Indexed: 01/23/2023]
Abstract
BACKGROUND Risk factor identification is a proven strategy in advancing treatments and preventive therapy for many chronic conditions. Quantifying the impact of those risk factors on health outcomes can consolidate and focus efforts on individuals with specific high-risk profiles. Using multiple risk factors and longitudinal outcomes in 2 independent cohorts, we developed and validated a risk score model to predict mortality in current and former cigarette smokers. METHODS We obtained extensive data on current and former smokers from the COPD Genetic Epidemiology (COPDGene®) study at enrollment. Based on physician input and model goodness-of-fit measures, a subset of variables was selected to fit final Weibull survival models separately for men and women. Coefficients and predictors were translated into a point system, allowing for easy computation of mortality risk scores and probabilities. We then used the SubPopulations and InteRmediate Outcome Measures In COPD Study (SPIROMICS) cohort for external validation of our model. RESULTS Of 9867 COPDGene participants with standard baseline data, 17.6% died over 10 years of follow-up, and 9074 of these participants had the full set of baseline predictors (standard plus 6-minute walk distance and computed tomography variables) available for full model fits. The average age of participants in the cohort was 60 for both men and women, and the average predicted 10-year mortality risk was 18% for women and 25% for men. Model time-integrated area under the receiver operating characteristic curve statistics demonstrated good predictive model accuracy (0.797 average), validated in the external cohort (0.756 average). Risk of mortality was impacted most by 6-minute walk distance, forced expiratory volume in 1 second and age, for both men and women. CONCLUSIONS Current and former smokers exhibited a wide range of mortality risk over a 10- year period. Our models can identify higher risk individuals who can be targeted for interventions to reduce risk of mortality, for participants with or without chronic obstructive pulmonary disease (COPD) using current Global initiative for obstructive Lung Disease (GOLD) criteria.
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Affiliation(s)
| | | | - Matthew Moll
- Brigham and Women’s Hospital, Boston, Massachusetts
| | | | | | | | | | | | - Richard Casaburi
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | | | | | - Ingo Ruczinski
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | | | - Harry B. Rossiter
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
- University of Leeds, Leeds, United Kingdom
| | - Mariaelena Occhipinti
- University of Florence, Florence, Italy
- *Dr. Occhipinti is now at the Imaging Institute, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | | | | | | | - Ken M. Kunisaki
- Minneapolis Veterans Administration Health Care System, Minnesota
| | | | | | | | | | - Sharon M. Lutz
- Harvard Medical School, Harvard University, Boston, Massachusetts
| | | | | | | | | | - Dawn L. DeMeo
- Brigham and Women’s Hospital, Boston, Massachusetts
- Harvard Medical School, Harvard University, Boston, Massachusetts
| | | | | | | | - Igor Barjaktarevic
- David Geffen School of Medicine, University of California-Los Angeles, Los Angeles
| | | | | | - Stephen P. Peters
- Wake Forest School of Medicine, Wake Forest University, Winston-Salem, North Carolina
| | - Victor E. Ortega
- Wake Forest School of Medicine, Wake Forest University, Winston-Salem, North Carolina
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33
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Moll M, Sakornsakolpat P, Shrine N, Hobbs BD, DeMeo DL, John C, Guyatt AL, McGeachie MJ, Gharib SA, Obeidat M, Lahousse L, Wijnant SRA, Brusselle G, Meyers DA, Bleecker ER, Li X, Tal-Singer R, Manichaikul A, Rich SS, Won S, Kim WJ, Do AR, Washko GR, Barr RG, Psaty BM, Bartz TM, Hansel NN, Barnes K, Hokanson JE, Crapo JD, Lynch D, Bakke P, Gulsvik A, Hall IP, Wain L, Weiss ST, Silverman EK, Dudbridge F, Tobin MD, Cho MH. Chronic obstructive pulmonary disease and related phenotypes: polygenic risk scores in population-based and case-control cohorts. Lancet Respir Med 2020; 8:696-708. [PMID: 32649918 PMCID: PMC7429152 DOI: 10.1016/s2213-2600(20)30101-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [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: 09/29/2019] [Revised: 01/24/2020] [Accepted: 02/17/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Genetic factors influence chronic obstructive pulmonary disease (COPD) risk, but the individual variants that have been identified have small effects. We hypothesised that a polygenic risk score using additional variants would predict COPD and associated phenotypes. METHODS We constructed a polygenic risk score using a genome-wide association study of lung function (FEV1 and FEV1/forced vital capacity [FVC]) from the UK Biobank and SpiroMeta. We tested this polygenic risk score in nine cohorts of multiple ethnicities for an association with moderate-to-severe COPD (defined as FEV1/FVC <0·7 and FEV1 <80% of predicted). Associations were tested using logistic regression models, adjusting for age, sex, height, smoking pack-years, and principal components of genetic ancestry. We assessed predictive performance of models by area under the curve. In a subset of studies, we also studied quantitative and qualitative CT imaging phenotypes that reflect parenchymal and airway pathology, and patterns of reduced lung growth. FINDINGS The polygenic risk score was associated with COPD in European (odds ratio [OR] per SD 1·81 [95% CI 1·74-1·88] and non-European (1·42 [1·34-1·51]) populations. Compared with the first decile, the tenth decile of the polygenic risk score was associated with COPD, with an OR of 7·99 (6·56-9·72) in European ancestry and 4·83 (3·45-6·77) in non-European ancestry cohorts. The polygenic risk score was superior to previously described genetic risk scores and, when combined with clinical risk factors (ie, age, sex, and smoking pack-years), showed improved prediction for COPD compared with a model comprising clinical risk factors alone (AUC 0·80 [0·79-0·81] vs 0·76 [0·75-0·76]). The polygenic risk score was associated with CT imaging phenotypes, including wall area percent, quantitative and qualitative measures of emphysema, local histogram emphysema patterns, and destructive emphysema subtypes. The polygenic risk score was associated with a reduced lung growth pattern. INTERPRETATION A risk score comprised of genetic variants can identify a small subset of individuals at markedly increased risk for moderate-to-severe COPD, emphysema subtypes associated with cigarette smoking, and patterns of reduced lung growth. FUNDING US National Institutes of Health, Wellcome Trust.
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Affiliation(s)
- Matthew Moll
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Phuwanat Sakornsakolpat
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Catherine John
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anna L Guyatt
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, Department of Medicine, University of Washington, Seattle, WA, USA; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ma'en Obeidat
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, Netherlands; Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Sara R A Wijnant
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, Netherlands; Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Guy Brusselle
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, Netherlands; Department of Respiratory Medicine, Erasmus Medical Centre, Rotterdam, Netherlands; Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | | | | | - Xingnan Li
- Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Ruth Tal-Singer
- GlaxoSmithKline Research and Development, Collegeville, PA, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Sungho Won
- Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, South Korea; Interdisciplinary Program of Bioinformatics, College of National Sciences, Seoul National University, Seoul, South Korea; Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Woo Jin Kim
- Department of Internal Medicine, Kangwon National University, Chuncheon, South Korea
| | - Ah Ra Do
- Interdisciplinary Program of Bioinformatics, College of National Sciences, Seoul National University, Seoul, South Korea
| | - George R Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - R Graham Barr
- Department of Medicine and Department of Epidemiology, Columbia University Medical Center, New York, NY, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA; Kaiser Permanente Washington Health Research Institute, Seattle, WA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Nadia N Hansel
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Kathleen Barnes
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - James D Crapo
- Division of Pulmonary, Critical Care, and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - David Lynch
- Department of Radiology, National Jewish Health, Denver, CO, USA
| | - Per Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Amund Gulsvik
- Division of Respiratory Medicine, Queen's Medical Centre, Nottingham, UK
| | - Ian P Hall
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Louise Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK; National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Frank Dudbridge
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Martin D Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK; National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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34
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Jiang Y, Chen S, Wang X, Liu M, Iacono WG, Hewitt JK, Hokanson JE, Krauter K, Laakso M, Li KW, Lutz SM, McGue M, Pandit A, Zajac GJ, Boehnke M, Abecasis GR, Vrieze SI, Jiang B, Zhan X, Liu DJ. Association Analysis and Meta-Analysis of Multi-Allelic Variants for Large-Scale Sequence Data. Genes (Basel) 2020; 11:genes11050586. [PMID: 32466134 PMCID: PMC7288273 DOI: 10.3390/genes11050586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/19/2020] [Accepted: 05/21/2020] [Indexed: 11/16/2022] Open
Abstract
There is great interest in understanding the impact of rare variants in human diseases using large sequence datasets. In deep sequence datasets of >10,000 samples, ~10% of the variant sites are observed to be multi-allelic. Many of the multi-allelic variants have been shown to be functional and disease-relevant. Proper analysis of multi-allelic variants is critical to the success of a sequencing study, but existing methods do not properly handle multi-allelic variants and can produce highly misleading association results. We discuss practical issues and methods to encode multi-allelic sites, conduct single-variant and gene-level association analyses, and perform meta-analysis for multi-allelic variants. We evaluated these methods through extensive simulations and the study of a large meta-analysis of ~18,000 samples on the cigarettes-per-day phenotype. We showed that our joint modeling approach provided an unbiased estimate of genetic effects, greatly improved the power of single-variant association tests among methods that can properly estimate allele effects, and enhanced gene-level tests over existing approaches. Software packages implementing these methods are available online.
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Affiliation(s)
- Yu Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033, USA; (Y.J.); (X.W.); (D.J.L.)
| | - Sai Chen
- Illumina Inc., 5200 Illuminay Way, San Diego, CA 92122, USA;
| | - Xingyan Wang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033, USA; (Y.J.); (X.W.); (D.J.L.)
| | - Mengzhen Liu
- Department of Psychology, University of Minnesota, Minneapolis, MN 55454, USA; (M.L.); (M.M.); (S.I.V.)
| | - William G. Iacono
- Department of Psychiatry, University of Minnesota, Minneapolis, MN 55454, USA;
| | - John K. Hewitt
- Institute for Behavioral Genetics, University of Colorado Boulder, Aurora, CO 80045, USA; (J.K.H.); (K.K.)
| | - John E. Hokanson
- Department of Epidemiology, School of Public Health, University of Colorado Denver, Aurora, CO 80045, USA;
| | - Kenneth Krauter
- Institute for Behavioral Genetics, University of Colorado Boulder, Aurora, CO 80045, USA; (J.K.H.); (K.K.)
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, 70211 Kuopio, Finland;
| | - Kevin W. Li
- Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; (K.W.L.); (A.P.); (G.J.M.Z.); (M.B.); (G.R.A.)
| | - Sharon M. Lutz
- Department of Biostatistics and Informatics, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA;
| | - Matthew McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN 55454, USA; (M.L.); (M.M.); (S.I.V.)
| | - Anita Pandit
- Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; (K.W.L.); (A.P.); (G.J.M.Z.); (M.B.); (G.R.A.)
| | - Gregory J.M. Zajac
- Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; (K.W.L.); (A.P.); (G.J.M.Z.); (M.B.); (G.R.A.)
| | - Michael Boehnke
- Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; (K.W.L.); (A.P.); (G.J.M.Z.); (M.B.); (G.R.A.)
| | - Goncalo R. Abecasis
- Center of Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA; (K.W.L.); (A.P.); (G.J.M.Z.); (M.B.); (G.R.A.)
| | - Scott I. Vrieze
- Department of Psychology, University of Minnesota, Minneapolis, MN 55454, USA; (M.L.); (M.M.); (S.I.V.)
| | - Bibo Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033, USA; (Y.J.); (X.W.); (D.J.L.)
- Correspondence: (B.J.); (X.Z.)
| | - Xiaowei Zhan
- Department of Clinical Science, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Correspondence: (B.J.); (X.Z.)
| | - Dajiang J. Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033, USA; (Y.J.); (X.W.); (D.J.L.)
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35
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Washko GR, Nardelli P, Ash SY, Rahaghi FN, Vegas Sanchez-Ferrero G, Come CE, Dransfield MT, Kalhan R, Han MK, Bhatt SP, Wells JM, Pistenmaa CL, Diaz AA, Ross JC, Rennard S, Querejeta Roca G, Shah AM, Young K, Kinney GL, Hokanson JE, Agustí A, San José Estépar R. Smaller Left Ventricle Size at Noncontrast CT Is Associated with Lower Mortality in COPDGene Participants. Radiology 2020; 296:208-215. [PMID: 32368963 PMCID: PMC7299752 DOI: 10.1148/radiol.2020191793] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Background Smokers with chronic obstructive pulmonary disease (COPD) have smaller left ventricles (LVs) due to reduced preload. Skeletal muscle wasting is also common in COPD, but less is known about its contribution to LV size. Purpose To explore the relationships between CT metrics of emphysema, venous vascular volume, and sarcopenia with the LV epicardial volume (LVEV) (myocardium and chamber) estimated from chest CT images in participants with COPD and then to determine the clinical relevance of the LVEV in multivariable models, including sex and anthropomorphic metrics. Materials and Methods The COPDGene study (ClinicalTrials.gov identifier: NCT00608764) is an ongoing prospective longitudinal observational investigation that began in 2006. LVEV, distal pulmonary venous blood volume for vessels smaller than 5 mm2 in cross section (BV5), CT emphysema, and pectoralis muscle area were retrospectively extracted from 3318 nongated, unenhanced COPDGene CT scans. Multivariable linear and Cox regression models were used to explore the association between emphysema, venous BV5, pectoralis muscle area, and LVEV as well as the association of LVEV with health status using the St George's Respiratory Questionnaire, 6-minute walk distance, and all-cause mortality. Results The median age of the cohort was 64 years (interquartile range, 57-70 years). Of the 2423 participants, 1806 were men and 617 were African American. The median LVEV between Global Initiative for Chronic Obstructive Lung Disease (GOLD) 1 and GOLD 4 COPD was reduced by 13.9% in women and 17.7% in men (P < .001 for both). In fully adjusted models, higher emphysema percentage (β = -4.2; 95% confidence interval [CI]: -5.0, -3.4; P < .001), venous BV5 (β = 7.0; 95% CI: 5.7, 8.2; P < .001), and pectoralis muscle area (β = 2.7; 95% CI: 1.2, 4.1; P < .001) were independently associated with reduced LVEV. Reductions in LVEV were associated with improved health status (β = 0.3; 95% CI: 0.1, 0.4) and 6-minute walk distance (β = -12.2; 95% CI: -15.2, -9.3). These effects were greater in women than in men. The effect of reduced LVEV on mortality (hazard ratio: 1.07; 95% CI: 1.05, 1.09) did not vary by sex. Conclusion In women more than men with chronic obstructive pulmonary disease, a reduction in the estimated left ventricle epicardial volume correlated with a loss of pulmonary venous vasculature, greater pectoralis muscle sarcopenia, and lower all-cause mortality. © RSNA, 2020 Online supplemental material is available for this article.
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Affiliation(s)
- George R Washko
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - Pietro Nardelli
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - Samuel Y Ash
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - Farbod N Rahaghi
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - Gonzalo Vegas Sanchez-Ferrero
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - Carolyn E Come
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - Mark T Dransfield
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - Ravi Kalhan
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - MeiLan K Han
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - Surya P Bhatt
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - J Michael Wells
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - Carrie L Pistenmaa
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - Alejandro A Diaz
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - James C Ross
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - Stephen Rennard
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - Gabriela Querejeta Roca
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - Amil M Shah
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - Kendra Young
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - Gregory L Kinney
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - John E Hokanson
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - Alvar Agustí
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | - Raúl San José Estépar
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
| | -
- From the Division of Pulmonary and Critical Care, Department of Medicine, Applied Chest Imaging Laboratory (G.R.W., S.Y.A., F.N.R., C.E.C., C.L.P., A.A.D.), Department of Radiology, Applied Chest Imaging Laboratory (P.N., G.V.S.F., J.C.R., R.S.J.E.), Department of Anesthesia (G.Q.R.), and Division of Cardiology (A.M.S.), Brigham and Women's Hospital, 1249 Boylston St, Boston, MA 02215; Lung Health Center, University of Alabama at Birmingham, Birmingham, Ala (M.T.D., S.P.B., J.M.W.); Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Ill (R.K.); Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Mich (M.K.H.); BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom (S.R.), Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Neb (S.R.); Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colo (K.Y., G.L.K., J.E.H.); and Respiratory Institute, Hospital Clinic, August Pi i Sunyer Biomedical Research Institute, Centro de Investigación Biomédica en Red Enfermedades Respiratorias, University of Barcelona, Barcelona, Spain (A.A.)
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Lutz SM, Hokanson JE. The Use of Mendelian Randomization to Determine the Role of Metabolic Traits on Urinary Albumin-to-Creatinine Ratio. Diabetes 2020; 69:862-863. [PMID: 32312903 PMCID: PMC7171963 DOI: 10.2337/dbi19-0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Sharon M Lutz
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - John E Hokanson
- Department of Epidemiology, University of Colorado, Anschutz Medical Campus, Aurora, CO
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Lutz SM, Frederiksen B, Begum F, McDonald MLN, Cho MH, Hobbs BD, Parker MM, DeMeo DL, Hersh CP, Ehringer MA, Young K, Jiang L, Foreman MG, Kinney GL, Make BJ, Lomas DA, Bakke P, Gulsvik A, Crapo JD, Silverman EK, Beaty TH, Hokanson JE. Common and Rare Variants Genetic Association Analysis of Cigarettes per Day Among Ever-Smokers in Chronic Obstructive Pulmonary Disease Cases and Controls. Nicotine Tob Res 2020; 21:714-722. [PMID: 29767774 DOI: 10.1093/ntr/nty095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 05/09/2018] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Cigarette smoking is a major environmental risk factor for many diseases, including chronic obstructive pulmonary disease (COPD). There are shared genetic influences on cigarette smoking and COPD. Genetic risk factors for cigarette smoking in cohorts enriched for COPD are largely unknown. METHODS We performed genome-wide association analyses for average cigarettes per day (CPD) across the Genetic Epidemiology of COPD (COPDGene) non-Hispanic white (NHW) (n = 6659) and African American (AA) (n = 3260), GenKOLS (the Genetics of Chronic Obstructive Lung Disease) (n = 1671), and ECLIPSE (the Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints) (n = 1942) cohorts. In addition, we performed exome array association analyses across the COPDGene NHW and AA cohorts. We considered analyses across the entire cohort and stratified by COPD case-control status. RESULTS We identified genome-wide significant associations for CPD on chromosome 15q25 across all cohorts (lowest p = 1.78 × 10-15), except in the COPDGene AA cohort alone. Previously reported associations on chromosome 19 had suggestive and directionally consistent associations (RAB4, p = 1.95 × 10-6; CYP2A7, p = 7.50 × 10-5; CYP2B6, p = 4.04 × 10-4). When we stratified by COPD case-control status, single nucleotide polymorphisms on chromosome 15q25 were nominally associated with both NHW COPD cases (β = 0.11, p = 5.58 × 10-4) and controls (β = 0.12, p = 3.86 × 10-5) For the gene-based exome array association analysis of rare variants, there were no exome-wide significant associations. For these previously replicated associations, the most significant results were among COPDGene NHW subjects for CYP2A7 (p = 5.2 × 10-4). CONCLUSIONS In a large genome-wide association study of both common variants and a gene-based association of rare coding variants in ever-smokers, we found genome-wide significant associations on chromosome 15q25 with CPD for common variants, but not for rare coding variants. These results were directionally consistent among COPD cases and controls. IMPLICATIONS We examined both common and rare coding variants associated with CPD in a large population of heavy smokers with and without COPD of NHW and AA descent. We replicated genome-wide significant associations on chromosome 15q25 with CPD for common variants among NHW subjects, but not for rare variants. We demonstrated for the first time that common variants on chromosome 15q25 associated with CPD are similar among COPD cases and controls. Previously reported associations on chromosome 19 showed suggestive and directionally consistent associations among common variants (RAB4, CYP2A7, and CYP2B6) and for rare variants (CYP2A7) among COPDGene NHW subjects. Although the genetic effect sizes for these single nucleotide polymorphisms on chromosome 15q25 are modest, we show that this creates a substantial smoking burden over the lifetime of a smoker.
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Affiliation(s)
- Sharon M Lutz
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Brittni Frederiksen
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Ferdouse Begum
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Merry-Lynn N McDonald
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Marissa A Ehringer
- Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, CO
| | - Kendra Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Lai Jiang
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | | | - Greg L Kinney
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Barry J Make
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO
| | - David A Lomas
- UCL Respiratory, University College London, London, UK
| | - Per Bakke
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Amund Gulsvik
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - James D Crapo
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO
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Lowe KE, Hokanson JE, Make BJ, Pratte KA, Regan EA, Silverman EK, Young KA, Kinney GL, Crapo JD. Letter to the Editor: Response by Authors. Chronic Obstr Pulm Dis 2020; 7:82-85. [PMID: 32324979 PMCID: PMC7454025 DOI: 10.15326/jcopdf.7.2.2020.0152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Katherine E. Lowe
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve School of Medicine, Cleveland, Ohio
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39
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Ragland MF, Benway CJ, Lutz SM, Bowler RP, Hecker J, Hokanson JE, Crapo JD, Castaldi PJ, DeMeo DL, Hersh CP, Hobbs BD, Lange C, Beaty TH, Cho MH, Silverman EK. Genetic Advances in Chronic Obstructive Pulmonary Disease. Insights from COPDGene. Am J Respir Crit Care Med 2020; 200:677-690. [PMID: 30908940 DOI: 10.1164/rccm.201808-1455so] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a common and progressive disease that is influenced by both genetic and environmental factors. For many years, knowledge of the genetic basis of COPD was limited to Mendelian syndromes, such as alpha-1 antitrypsin deficiency and cutis laxa, caused by rare genetic variants. Over the past decade, the proliferation of genome-wide association studies, the accessibility of whole-genome sequencing, and the development of novel methods for analyzing genetic variation data have led to a substantial increase in the understanding of genetic variants that play a role in COPD susceptibility and COPD-related phenotypes. COPDGene (Genetic Epidemiology of COPD), a multicenter, longitudinal study of over 10,000 current and former cigarette smokers, has been pivotal to these breakthroughs in understanding the genetic basis of COPD. To date, over 20 genetic loci have been convincingly associated with COPD affection status, with additional loci demonstrating association with COPD-related phenotypes such as emphysema, chronic bronchitis, and hypoxemia. In this review, we discuss the contributions of the COPDGene study to the discovery of these genetic associations as well as the ongoing genetic investigations of COPD subtypes, protein biomarkers, and post-genome-wide association study analysis.
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Affiliation(s)
- Margaret F Ragland
- Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, and
| | | | | | | | - Julian Hecker
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts; and
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado
| | | | | | - Dawn L DeMeo
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Craig P Hersh
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Brian D Hobbs
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Christoph Lange
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts; and
| | - Terri H Beaty
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - Michael H Cho
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Edwin K Silverman
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
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40
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Lutz SM, Sordillo JE, Hokanson JE, Chen Wu A, Lange C. The effects of misspecification of the mediator and outcome in mediation analysis. Genet Epidemiol 2020; 44:400-403. [PMID: 32166765 DOI: 10.1002/gepi.22289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/28/2020] [Accepted: 02/19/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Sharon M Lutz
- Department of Population Medicine, PRecisiOn Medicine Translational Research Center, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Joanne E Sordillo
- Department of Population Medicine, PRecisiOn Medicine Translational Research Center, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts
| | - John E Hokanson
- Department of Epidemiology, University of Colorado, Boulder, Colorado
| | - Ann Chen Wu
- Department of Population Medicine, PRecisiOn Medicine Translational Research Center, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts
| | - Christoph Lange
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
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Pompe E, Strand M, van Rikxoort EM, Hoffman EA, Barr RG, Charbonnier JP, Humphries S, Han MK, Hokanson JE, Make BJ, Regan EA, Silverman EK, Crapo JD, Lynch DA. Five-year Progression of Emphysema and Air Trapping at CT in Smokers with and Those without Chronic Obstructive Pulmonary Disease: Results from the COPDGene Study. Radiology 2020; 295:218-226. [PMID: 32013794 DOI: 10.1148/radiol.2020191429] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background CT is used to quantify abnormal changes in the lung parenchyma of smokers that might overlap chronic obstructive pulmonary disease (COPD), but studies on the progression of expiratory air trapping in smokers are scarce. Purpose To evaluate the relationship between longitudinal changes in forced expiratory volume in 1 second (FEV1) and CT-quantified emphysema and air trapping in smokers. Materials and Methods Cigarette smokers with and those without COPD participating in the multicenter observational COPDGene study were evaluated. Subjects underwent inspiratory and expiratory chest CT and spirometry at baseline and 5-year follow-up. Emphysema was quantified by using adjusted lung density (ALD). Air trapping was quantified by using mean lung density at expiratory CT and CT-measured functional residual capacity-to-total lung volume ratio. Linear models were used to regress quantitative CT measurements taken 5 years apart, and models were fit with and without adding FEV1 as a predictor. Analyses were stratified by Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage (GOLD 0, no COPD; GOLD 1, mild COPD; GOLD 2, moderate COPD; GOLD 3, severe COPD; GOLD 4, very severe COPD). Subjects with preserved FEV1-to-forced vital capacity ratio and reduced FEV1 percentage predicted were categorized as having preserved ratio impaired spirometry (PRISm). Results A total of 4211 subjects (503 with PRISm; 2034 with GOLD 0, 388 with GOLD 1, 816 with GOLD 2, 381 with GOLD 3, 89 with GOLD 4) were evaluated. ALD decreased by 1.7 g/L (95% confidence interval [CI]: -2.5, -0.9) in subjects with GOLD 0 at baseline and by 5.3 g/L (95% CI: -6.2, -4.4) in those with GOLD 1-4 (P < .001 for both). When adjusted for changes in FEV1, corresponding numbers were -2.2 (95% CI: -3.0, -1.3) and -4.6 g/L (95% CI: -5.6, -3.4) (P < .001 for both). Progression in air trapping was identified only in GOLD stage 2-4. Approximately 33%-50% of changes in air trapping in GOLD stages 2-4 were accounted for by changes in FEV1. Conclusion CT measures of emphysema and air trapping increased over 5 years in smokers. Forced expiratory volume in one second accounted for less than 10% of emphysema progression and less than 50% of air trapping progression detected at CT. © RSNA, 2020 Online supplemental material is available for this article.
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Affiliation(s)
- Esther Pompe
- From the Department of Radiology, University Medical Center Utrecht, Heidelberglaan 100, PO 85500, Postbox E.03.511, Utrecht, Utrecht 3508 GA, the Netherlands (E.P.); Division of Biostatistics and Bioinformatics (M.S., B.J.M.), Department of Radiology (S.H., D.A.L.), Division of Rheumatology, Department of Medicine (E.A.R.), and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (J.D.C.), National Jewish Health, Denver, Colo; Thirona, Nijmegen, the Netherlands (E.M.v.R.); Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands (E.M.v.R., J.P.C.); Departments of Biomedical Engineering, Radiology, and Internal Medicine, University of Iowa, Iowa City, Iowa (E.A.H.); Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY (R.G.B.); Division of Pulmonary and Critical Care, University of Michigan Health System, Ann Arbor, Mich (M.K.H.); Department of Epidemiology, University of Colorado Denver, Denver, Colo (J.E.H.); and Channing Division of Network Medicine (E.K.S.) and Division of Pulmonary and Critical Care Medicine, Department of Medicine (E.K.S.), Brigham and Women's Hospital, Boston, Mass
| | - Matthew Strand
- From the Department of Radiology, University Medical Center Utrecht, Heidelberglaan 100, PO 85500, Postbox E.03.511, Utrecht, Utrecht 3508 GA, the Netherlands (E.P.); Division of Biostatistics and Bioinformatics (M.S., B.J.M.), Department of Radiology (S.H., D.A.L.), Division of Rheumatology, Department of Medicine (E.A.R.), and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (J.D.C.), National Jewish Health, Denver, Colo; Thirona, Nijmegen, the Netherlands (E.M.v.R.); Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands (E.M.v.R., J.P.C.); Departments of Biomedical Engineering, Radiology, and Internal Medicine, University of Iowa, Iowa City, Iowa (E.A.H.); Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY (R.G.B.); Division of Pulmonary and Critical Care, University of Michigan Health System, Ann Arbor, Mich (M.K.H.); Department of Epidemiology, University of Colorado Denver, Denver, Colo (J.E.H.); and Channing Division of Network Medicine (E.K.S.) and Division of Pulmonary and Critical Care Medicine, Department of Medicine (E.K.S.), Brigham and Women's Hospital, Boston, Mass
| | - Eva M van Rikxoort
- From the Department of Radiology, University Medical Center Utrecht, Heidelberglaan 100, PO 85500, Postbox E.03.511, Utrecht, Utrecht 3508 GA, the Netherlands (E.P.); Division of Biostatistics and Bioinformatics (M.S., B.J.M.), Department of Radiology (S.H., D.A.L.), Division of Rheumatology, Department of Medicine (E.A.R.), and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (J.D.C.), National Jewish Health, Denver, Colo; Thirona, Nijmegen, the Netherlands (E.M.v.R.); Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands (E.M.v.R., J.P.C.); Departments of Biomedical Engineering, Radiology, and Internal Medicine, University of Iowa, Iowa City, Iowa (E.A.H.); Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY (R.G.B.); Division of Pulmonary and Critical Care, University of Michigan Health System, Ann Arbor, Mich (M.K.H.); Department of Epidemiology, University of Colorado Denver, Denver, Colo (J.E.H.); and Channing Division of Network Medicine (E.K.S.) and Division of Pulmonary and Critical Care Medicine, Department of Medicine (E.K.S.), Brigham and Women's Hospital, Boston, Mass
| | - Eric A Hoffman
- From the Department of Radiology, University Medical Center Utrecht, Heidelberglaan 100, PO 85500, Postbox E.03.511, Utrecht, Utrecht 3508 GA, the Netherlands (E.P.); Division of Biostatistics and Bioinformatics (M.S., B.J.M.), Department of Radiology (S.H., D.A.L.), Division of Rheumatology, Department of Medicine (E.A.R.), and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (J.D.C.), National Jewish Health, Denver, Colo; Thirona, Nijmegen, the Netherlands (E.M.v.R.); Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands (E.M.v.R., J.P.C.); Departments of Biomedical Engineering, Radiology, and Internal Medicine, University of Iowa, Iowa City, Iowa (E.A.H.); Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY (R.G.B.); Division of Pulmonary and Critical Care, University of Michigan Health System, Ann Arbor, Mich (M.K.H.); Department of Epidemiology, University of Colorado Denver, Denver, Colo (J.E.H.); and Channing Division of Network Medicine (E.K.S.) and Division of Pulmonary and Critical Care Medicine, Department of Medicine (E.K.S.), Brigham and Women's Hospital, Boston, Mass
| | - R Graham Barr
- From the Department of Radiology, University Medical Center Utrecht, Heidelberglaan 100, PO 85500, Postbox E.03.511, Utrecht, Utrecht 3508 GA, the Netherlands (E.P.); Division of Biostatistics and Bioinformatics (M.S., B.J.M.), Department of Radiology (S.H., D.A.L.), Division of Rheumatology, Department of Medicine (E.A.R.), and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (J.D.C.), National Jewish Health, Denver, Colo; Thirona, Nijmegen, the Netherlands (E.M.v.R.); Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands (E.M.v.R., J.P.C.); Departments of Biomedical Engineering, Radiology, and Internal Medicine, University of Iowa, Iowa City, Iowa (E.A.H.); Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY (R.G.B.); Division of Pulmonary and Critical Care, University of Michigan Health System, Ann Arbor, Mich (M.K.H.); Department of Epidemiology, University of Colorado Denver, Denver, Colo (J.E.H.); and Channing Division of Network Medicine (E.K.S.) and Division of Pulmonary and Critical Care Medicine, Department of Medicine (E.K.S.), Brigham and Women's Hospital, Boston, Mass
| | - Jean Paul Charbonnier
- From the Department of Radiology, University Medical Center Utrecht, Heidelberglaan 100, PO 85500, Postbox E.03.511, Utrecht, Utrecht 3508 GA, the Netherlands (E.P.); Division of Biostatistics and Bioinformatics (M.S., B.J.M.), Department of Radiology (S.H., D.A.L.), Division of Rheumatology, Department of Medicine (E.A.R.), and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (J.D.C.), National Jewish Health, Denver, Colo; Thirona, Nijmegen, the Netherlands (E.M.v.R.); Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands (E.M.v.R., J.P.C.); Departments of Biomedical Engineering, Radiology, and Internal Medicine, University of Iowa, Iowa City, Iowa (E.A.H.); Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY (R.G.B.); Division of Pulmonary and Critical Care, University of Michigan Health System, Ann Arbor, Mich (M.K.H.); Department of Epidemiology, University of Colorado Denver, Denver, Colo (J.E.H.); and Channing Division of Network Medicine (E.K.S.) and Division of Pulmonary and Critical Care Medicine, Department of Medicine (E.K.S.), Brigham and Women's Hospital, Boston, Mass
| | - Stephen Humphries
- From the Department of Radiology, University Medical Center Utrecht, Heidelberglaan 100, PO 85500, Postbox E.03.511, Utrecht, Utrecht 3508 GA, the Netherlands (E.P.); Division of Biostatistics and Bioinformatics (M.S., B.J.M.), Department of Radiology (S.H., D.A.L.), Division of Rheumatology, Department of Medicine (E.A.R.), and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (J.D.C.), National Jewish Health, Denver, Colo; Thirona, Nijmegen, the Netherlands (E.M.v.R.); Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands (E.M.v.R., J.P.C.); Departments of Biomedical Engineering, Radiology, and Internal Medicine, University of Iowa, Iowa City, Iowa (E.A.H.); Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY (R.G.B.); Division of Pulmonary and Critical Care, University of Michigan Health System, Ann Arbor, Mich (M.K.H.); Department of Epidemiology, University of Colorado Denver, Denver, Colo (J.E.H.); and Channing Division of Network Medicine (E.K.S.) and Division of Pulmonary and Critical Care Medicine, Department of Medicine (E.K.S.), Brigham and Women's Hospital, Boston, Mass
| | - MeiLan K Han
- From the Department of Radiology, University Medical Center Utrecht, Heidelberglaan 100, PO 85500, Postbox E.03.511, Utrecht, Utrecht 3508 GA, the Netherlands (E.P.); Division of Biostatistics and Bioinformatics (M.S., B.J.M.), Department of Radiology (S.H., D.A.L.), Division of Rheumatology, Department of Medicine (E.A.R.), and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (J.D.C.), National Jewish Health, Denver, Colo; Thirona, Nijmegen, the Netherlands (E.M.v.R.); Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands (E.M.v.R., J.P.C.); Departments of Biomedical Engineering, Radiology, and Internal Medicine, University of Iowa, Iowa City, Iowa (E.A.H.); Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY (R.G.B.); Division of Pulmonary and Critical Care, University of Michigan Health System, Ann Arbor, Mich (M.K.H.); Department of Epidemiology, University of Colorado Denver, Denver, Colo (J.E.H.); and Channing Division of Network Medicine (E.K.S.) and Division of Pulmonary and Critical Care Medicine, Department of Medicine (E.K.S.), Brigham and Women's Hospital, Boston, Mass
| | - John E Hokanson
- From the Department of Radiology, University Medical Center Utrecht, Heidelberglaan 100, PO 85500, Postbox E.03.511, Utrecht, Utrecht 3508 GA, the Netherlands (E.P.); Division of Biostatistics and Bioinformatics (M.S., B.J.M.), Department of Radiology (S.H., D.A.L.), Division of Rheumatology, Department of Medicine (E.A.R.), and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (J.D.C.), National Jewish Health, Denver, Colo; Thirona, Nijmegen, the Netherlands (E.M.v.R.); Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands (E.M.v.R., J.P.C.); Departments of Biomedical Engineering, Radiology, and Internal Medicine, University of Iowa, Iowa City, Iowa (E.A.H.); Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY (R.G.B.); Division of Pulmonary and Critical Care, University of Michigan Health System, Ann Arbor, Mich (M.K.H.); Department of Epidemiology, University of Colorado Denver, Denver, Colo (J.E.H.); and Channing Division of Network Medicine (E.K.S.) and Division of Pulmonary and Critical Care Medicine, Department of Medicine (E.K.S.), Brigham and Women's Hospital, Boston, Mass
| | - Barry J Make
- From the Department of Radiology, University Medical Center Utrecht, Heidelberglaan 100, PO 85500, Postbox E.03.511, Utrecht, Utrecht 3508 GA, the Netherlands (E.P.); Division of Biostatistics and Bioinformatics (M.S., B.J.M.), Department of Radiology (S.H., D.A.L.), Division of Rheumatology, Department of Medicine (E.A.R.), and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (J.D.C.), National Jewish Health, Denver, Colo; Thirona, Nijmegen, the Netherlands (E.M.v.R.); Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands (E.M.v.R., J.P.C.); Departments of Biomedical Engineering, Radiology, and Internal Medicine, University of Iowa, Iowa City, Iowa (E.A.H.); Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY (R.G.B.); Division of Pulmonary and Critical Care, University of Michigan Health System, Ann Arbor, Mich (M.K.H.); Department of Epidemiology, University of Colorado Denver, Denver, Colo (J.E.H.); and Channing Division of Network Medicine (E.K.S.) and Division of Pulmonary and Critical Care Medicine, Department of Medicine (E.K.S.), Brigham and Women's Hospital, Boston, Mass
| | - Elizabeth A Regan
- From the Department of Radiology, University Medical Center Utrecht, Heidelberglaan 100, PO 85500, Postbox E.03.511, Utrecht, Utrecht 3508 GA, the Netherlands (E.P.); Division of Biostatistics and Bioinformatics (M.S., B.J.M.), Department of Radiology (S.H., D.A.L.), Division of Rheumatology, Department of Medicine (E.A.R.), and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (J.D.C.), National Jewish Health, Denver, Colo; Thirona, Nijmegen, the Netherlands (E.M.v.R.); Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands (E.M.v.R., J.P.C.); Departments of Biomedical Engineering, Radiology, and Internal Medicine, University of Iowa, Iowa City, Iowa (E.A.H.); Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY (R.G.B.); Division of Pulmonary and Critical Care, University of Michigan Health System, Ann Arbor, Mich (M.K.H.); Department of Epidemiology, University of Colorado Denver, Denver, Colo (J.E.H.); and Channing Division of Network Medicine (E.K.S.) and Division of Pulmonary and Critical Care Medicine, Department of Medicine (E.K.S.), Brigham and Women's Hospital, Boston, Mass
| | - Edwin K Silverman
- From the Department of Radiology, University Medical Center Utrecht, Heidelberglaan 100, PO 85500, Postbox E.03.511, Utrecht, Utrecht 3508 GA, the Netherlands (E.P.); Division of Biostatistics and Bioinformatics (M.S., B.J.M.), Department of Radiology (S.H., D.A.L.), Division of Rheumatology, Department of Medicine (E.A.R.), and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (J.D.C.), National Jewish Health, Denver, Colo; Thirona, Nijmegen, the Netherlands (E.M.v.R.); Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands (E.M.v.R., J.P.C.); Departments of Biomedical Engineering, Radiology, and Internal Medicine, University of Iowa, Iowa City, Iowa (E.A.H.); Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY (R.G.B.); Division of Pulmonary and Critical Care, University of Michigan Health System, Ann Arbor, Mich (M.K.H.); Department of Epidemiology, University of Colorado Denver, Denver, Colo (J.E.H.); and Channing Division of Network Medicine (E.K.S.) and Division of Pulmonary and Critical Care Medicine, Department of Medicine (E.K.S.), Brigham and Women's Hospital, Boston, Mass
| | - James D Crapo
- From the Department of Radiology, University Medical Center Utrecht, Heidelberglaan 100, PO 85500, Postbox E.03.511, Utrecht, Utrecht 3508 GA, the Netherlands (E.P.); Division of Biostatistics and Bioinformatics (M.S., B.J.M.), Department of Radiology (S.H., D.A.L.), Division of Rheumatology, Department of Medicine (E.A.R.), and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (J.D.C.), National Jewish Health, Denver, Colo; Thirona, Nijmegen, the Netherlands (E.M.v.R.); Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands (E.M.v.R., J.P.C.); Departments of Biomedical Engineering, Radiology, and Internal Medicine, University of Iowa, Iowa City, Iowa (E.A.H.); Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY (R.G.B.); Division of Pulmonary and Critical Care, University of Michigan Health System, Ann Arbor, Mich (M.K.H.); Department of Epidemiology, University of Colorado Denver, Denver, Colo (J.E.H.); and Channing Division of Network Medicine (E.K.S.) and Division of Pulmonary and Critical Care Medicine, Department of Medicine (E.K.S.), Brigham and Women's Hospital, Boston, Mass
| | - David A Lynch
- From the Department of Radiology, University Medical Center Utrecht, Heidelberglaan 100, PO 85500, Postbox E.03.511, Utrecht, Utrecht 3508 GA, the Netherlands (E.P.); Division of Biostatistics and Bioinformatics (M.S., B.J.M.), Department of Radiology (S.H., D.A.L.), Division of Rheumatology, Department of Medicine (E.A.R.), and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (J.D.C.), National Jewish Health, Denver, Colo; Thirona, Nijmegen, the Netherlands (E.M.v.R.); Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands (E.M.v.R., J.P.C.); Departments of Biomedical Engineering, Radiology, and Internal Medicine, University of Iowa, Iowa City, Iowa (E.A.H.); Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY (R.G.B.); Division of Pulmonary and Critical Care, University of Michigan Health System, Ann Arbor, Mich (M.K.H.); Department of Epidemiology, University of Colorado Denver, Denver, Colo (J.E.H.); and Channing Division of Network Medicine (E.K.S.) and Division of Pulmonary and Critical Care Medicine, Department of Medicine (E.K.S.), Brigham and Women's Hospital, Boston, Mass
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- From the Department of Radiology, University Medical Center Utrecht, Heidelberglaan 100, PO 85500, Postbox E.03.511, Utrecht, Utrecht 3508 GA, the Netherlands (E.P.); Division of Biostatistics and Bioinformatics (M.S., B.J.M.), Department of Radiology (S.H., D.A.L.), Division of Rheumatology, Department of Medicine (E.A.R.), and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine (J.D.C.), National Jewish Health, Denver, Colo; Thirona, Nijmegen, the Netherlands (E.M.v.R.); Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands (E.M.v.R., J.P.C.); Departments of Biomedical Engineering, Radiology, and Internal Medicine, University of Iowa, Iowa City, Iowa (E.A.H.); Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY (R.G.B.); Division of Pulmonary and Critical Care, University of Michigan Health System, Ann Arbor, Mich (M.K.H.); Department of Epidemiology, University of Colorado Denver, Denver, Colo (J.E.H.); and Channing Division of Network Medicine (E.K.S.) and Division of Pulmonary and Critical Care Medicine, Department of Medicine (E.K.S.), Brigham and Women's Hospital, Boston, Mass
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Moll M, Regan EA, Hokanson JE, Lutz SM, Silverman EK, Crapo JD, Make BJ, DeMeo DL. The Association of Multiparity with Lung Function and Chronic Obstructive Pulmonary Disease-Related Phenotypes. Chronic Obstr Pulm Dis 2020; 7:86-98. [PMID: 32324980 PMCID: PMC7454017 DOI: 10.15326/jcopdf.7.2.2019.0166] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND Apparent increased female susceptibility to chronic obstructive pulmonary disease (COPD) suggests sex hormones modulate disease pathogenesis. Little is known about associations between multiparity and lung function in smokers. RESEARCH QUESTION We hypothesized that multiparity is associated with lung function and measures of emphysema and airway disease. STUDY DESIGN AND METHODS Utilizing female participants from the 5-year follow up of the COPD Genetic Epidemiology (COPDGene®) study we performed multivariable linear regressions to assess the effect of multiparity and number of pregnancies on forced expiratory volume in 1 second (FEV1) percentage of predicted (% predicted), FEV1/forced vital capacity (FVC), percent emphysema on computed tomography (CT) scans, and Pi10, a measure of airway thickening. We sampled never smokers and those with lower smoking exposure from the National Health and Nutrition Examination Survey (NHANES) 2011-2012 dataset. RESULTS We included 1820 participants from COPDGene® and 418 participants from NHANES (321 never smokers, 97 ever smokers). In COPDGene®, multiparity (beta coefficient [β] = -3.8, 95% confidence interval [CI]: [-6.5, -1.1], p = 0.005) and higher number of pregnancies were associated with lower FEV1 % predicted. Multiparity was not associated with percent emphysema or Pi10. In individuals with no or mild obstruction, multiparity was associated with lower FEV1 % predicted. There was an interaction with multiparity and age on FEV1 % predicted (p = 0.025). In NHANES, there was no association between multiparity and FEV1 % predicted in never smokers or the lower smoking exposure group. INTERPRETATION Multiparity was associated with lower FEV1 % predicted in current and former smokers in COPDGene® study participants. These preliminary results emphasize the importance of smoking abstinence in women of child-bearing age.
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Affiliation(s)
- Matthew Moll
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts,Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | | | - John E. Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora
| | - Sharon M. Lutz
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, Massachusetts
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts,Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts,Harvard Medical School, Boston, Massachusetts
| | - James D. Crapo
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, Colorado
| | - Barry J. Make
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, Colorado
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts,Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
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Castaldi PJ, Boueiz A, Yun J, Estepar RSJ, Ross JC, Washko G, Cho MH, Hersh CP, Kinney GL, Young KA, Regan EA, Lynch DA, Criner GJ, Dy JG, Rennard SI, Casaburi R, Make BJ, Crapo J, Silverman EK, Hokanson JE. Machine Learning Characterization of COPD Subtypes: Insights From the COPDGene Study. Chest 2019; 157:1147-1157. [PMID: 31887283 DOI: 10.1016/j.chest.2019.11.039] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/18/2019] [Accepted: 11/29/2019] [Indexed: 12/17/2022] Open
Abstract
COPD is a heterogeneous syndrome. Many COPD subtypes have been proposed, but there is not yet consensus on how many COPD subtypes there are and how they should be defined. The COPD Genetic Epidemiology Study (COPDGene), which has generated 10-year longitudinal chest imaging, spirometry, and molecular data, is a rich resource for relating COPD phenotypes to underlying genetic and molecular mechanisms. In this article, we place COPDGene clustering studies in context with other highly cited COPD clustering studies, and summarize the main COPD subtype findings from COPDGene. First, most manifestations of COPD occur along a continuum, which explains why continuous aspects of COPD or disease axes may be more accurate and reproducible than subtypes identified through clustering methods. Second, continuous COPD-related measures can be used to create subgroups through the use of predictive models to define cut-points, and we review COPDGene research on blood eosinophil count thresholds as a specific example. Third, COPD phenotypes identified or prioritized through machine learning methods have led to novel biological discoveries, including novel emphysema genetic risk variants and systemic inflammatory subtypes of COPD. Fourth, trajectory-based COPD subtyping captures differences in the longitudinal evolution of COPD, addressing a major limitation of clustering analyses that are confounded by disease severity. Ongoing longitudinal characterization of subjects in COPDGene will provide useful insights about the relationship between lung imaging parameters, molecular markers, and COPD progression that will enable the identification of subtypes based on underlying disease processes and distinct patterns of disease progression, with the potential to improve the clinical relevance and reproducibility of COPD subtypes.
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Affiliation(s)
- Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; General Medicine and Primary Care, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.
| | - Adel Boueiz
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Jeong Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Raul San Jose Estepar
- Applied Chest Imaging Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - James C Ross
- Applied Chest Imaging Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - George Washko
- Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Applied Chest Imaging Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Gregory L Kinney
- Department of Epidemiology, University of Colorado, Denver, Aurora, CO
| | - Kendra A Young
- Department of Epidemiology, University of Colorado, Denver, Aurora, CO
| | | | - David A Lynch
- Department of Radiology, National Jewish Health, Denver, CO
| | - Gerald J Criner
- Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Jennifer G Dy
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA
| | - Stephen I Rennard
- Pulmonary and Critical Care Medicine, University of Nebraska Medical Center, Omaha, NE
| | - Richard Casaburi
- Rehabilitation Clinical Trials Center, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA
| | | | | | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - John E Hokanson
- Department of Epidemiology, University of Colorado, Denver, Aurora, CO
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Lowe KE, Regan EA, Anzueto A, Austin E, Austin JHM, Beaty TH, Benos PV, Benway CJ, Bhatt SP, Bleecker ER, Bodduluri S, Bon J, Boriek AM, Boueiz ARE, Bowler RP, Budoff M, Casaburi R, Castaldi PJ, Charbonnier JP, Cho MH, Comellas A, Conrad D, Costa Davis C, Criner GJ, Curran-Everett D, Curtis JL, DeMeo DL, Diaz AA, Dransfield MT, Dy JG, Fawzy A, Fleming M, Flenaugh EL, Foreman MG, Fortis S, Gebrekristos H, Grant S, Grenier PA, Gu T, Gupta A, Han MK, Hanania NA, Hansel NN, Hayden LP, Hersh CP, Hobbs BD, Hoffman EA, Hogg JC, Hokanson JE, Hoth KF, Hsiao A, Humphries S, Jacobs K, Jacobson FL, Kazerooni EA, Kim V, Kim WJ, Kinney GL, Koegler H, Lutz SM, Lynch DA, MacIntye Jr. NR, Make BJ, Marchetti N, Martinez FJ, Maselli DJ, Mathews AM, McCormack MC, McDonald MLN, McEvoy CE, Moll M, Molye SS, Murray S, Nath H, Newell Jr. JD, Occhipinti M, Paoletti M, Parekh T, Pistolesi M, Pratte KA, Putcha N, Ragland M, Reinhardt JM, Rennard SI, Rosiello RA, Ross JC, Rossiter HB, Ruczinski I, San Jose Estepar R, Sciurba FC, Sieren JC, Singh H, Soler X, Steiner RM, Strand MJ, Stringer WW, Tal-Singer R, Thomashow B, Vegas Sánchez-Ferrero G, Walsh JW, Wan ES, Washko GR, Michael Wells J, Wendt CH, Westney G, Wilson A, Wise RA, Yen A, Young K, Yun J, Silverman EK, Crapo JD. COPDGene ® 2019: Redefining the Diagnosis of Chronic Obstructive Pulmonary Disease. Chronic Obstr Pulm Dis 2019; 6:384-399. [PMID: 31710793 PMCID: PMC7020846 DOI: 10.15326/jcopdf.6.5.2019.0149] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/11/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) remains a major cause of morbidity and mortality. Present-day diagnostic criteria are largely based solely on spirometric criteria. Accumulating evidence has identified a substantial number of individuals without spirometric evidence of COPD who suffer from respiratory symptoms and/or increased morbidity and mortality. There is a clear need for an expanded definition of COPD that is linked to physiologic, structural (computed tomography [CT]) and clinical evidence of disease. Using data from the COPD Genetic Epidemiology study (COPDGene®), we hypothesized that an integrated approach that includes environmental exposure, clinical symptoms, chest CT imaging and spirometry better defines disease and captures the likelihood of progression of respiratory obstruction and mortality. METHODS Four key disease characteristics - environmental exposure (cigarette smoking), clinical symptoms (dyspnea and/or chronic bronchitis), chest CT imaging abnormalities (emphysema, gas trapping and/or airway wall thickening), and abnormal spirometry - were evaluated in a group of 8784 current and former smokers who were participants in COPDGene® Phase 1. Using these 4 disease characteristics, 8 categories of participants were identified and evaluated for odds of spirometric disease progression (FEV1 > 350 ml loss over 5 years), and the hazard ratio for all-cause mortality was examined. RESULTS Using smokers without symptoms, CT imaging abnormalities or airflow obstruction as the reference population, individuals were classified as Possible COPD, Probable COPD and Definite COPD. Current Global initiative for obstructive Lung Disease (GOLD) criteria would diagnose 4062 (46%) of the 8784 study participants with COPD. The proposed COPDGene® 2019 diagnostic criteria would add an additional 3144 participants. Under the new criteria, 82% of the 8784 study participants would be diagnosed with Possible, Probable or Definite COPD. These COPD groups showed increased risk of disease progression and mortality. Mortality increased in patients as the number of their COPD characteristics increased, with a maximum hazard ratio for all cause-mortality of 5.18 (95% confidence interval [CI]: 4.15-6.48) in those with all 4 disease characteristics. CONCLUSIONS A substantial portion of smokers with respiratory symptoms and imaging abnormalities do not manifest spirometric obstruction as defined by population normals. These individuals are at significant risk of death and spirometric disease progression. We propose to redefine the diagnosis of COPD through an integrated approach using environmental exposure, clinical symptoms, CT imaging and spirometric criteria. These expanded criteria offer the potential to stimulate both current and future interventions that could slow or halt disease progression in patients before disability or irreversible lung structural changes develop.
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Affiliation(s)
- Katherine E. Lowe
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve School of Medicine, Cleveland, Ohio
| | | | | | | | | | | | | | | | | | | | | | - Jessica Bon
- University of Pittsburgh, Pittsburgh, Pennsylvania
- VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania
| | | | | | | | - Matthew Budoff
- Los Angeles Biomedical Research Institute at Harbor- University of California Los Angeles Medical Center, Torrance
| | - Richard Casaburi
- Los Angeles Biomedical Research Institute at Harbor- University of California Los Angeles Medical Center, Torrance
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Margaret Fleming
- Novartis Institute for Biomedical Research, Cambridge, Massachusetts
| | | | | | | | | | - Sarah Grant
- Novartis Institute for Biomedical Research, Cambridge, Massachusetts
| | | | - Tian Gu
- University of Michigan, Ann Arbor
| | - Abhya Gupta
- Boehringer Ingelheim, Biberach an der Riss, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Victor Kim
- Temple University, Philadelphia, Pennsylvania
| | - Woo Jin Kim
- Kangwon National University, Chuncheon, Korea
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Matthew Moll
- Brigham and Women's Hospital, Boston, Massachusetts
| | | | | | | | | | | | | | | | | | | | | | | | | | - Stephen I. Rennard
- AstraZeneca, Cambridge, United Kingdom
- University of Nebraska Medical Center, Omaha
| | | | | | - Harry B. Rossiter
- Los Angeles Biomedical Research Institute at Harbor- University of California Los Angeles Medical Center, Torrance
- University of Leeds, Leeds, United Kingdom
| | | | | | | | | | | | - Xavier Soler
- University of California at San Diego
- GlaxoSmithKline, Research Triangle Park, North Carolina
| | | | | | - William W. Stringer
- Los Angeles Biomedical Research Institute at Harbor- University of California Los Angeles Medical Center, Torrance
| | | | | | | | | | - Emily S. Wan
- Brigham and Women's Hospital, Boston, Massachusetts
- VA Boston Healthcare System, Jamaica Plain, Massachusetts
| | | | | | | | | | | | | | | | - Kendra Young
- University of Colorado Anschutz Medical Campus, Aurora
| | - Jeong Yun
- Brigham and Women's Hospital, Boston, Massachusetts
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Budoff MJ, Lutz SM, Kinney GL, Young KA, Hokanson JE, Barr RG, Steiner R, Nath H, Lopez-Garcia C, Duca LM, Rahmani S, Osawa K, Regan EA, Li D, Casaburi R. Coronary Artery Calcium on Noncontrast Thoracic Computerized Tomography Scans and All-Cause Mortality. Circulation 2019; 138:2437-2438. [PMID: 30571584 DOI: 10.1161/circulationaha.118.036835] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Matthew J Budoff
- Department of Medicine, Los Angeles Biomedical Research Institute, Torrance, CA (M.J.B., C.L.-G., S.R., K.O., D.L., R.C.)
| | - Sharon M Lutz
- Department of Epidemiology (S.M.L., L.M.D., E.A.R.), University of Colorado Anschutz Medical Campus, Aurora.,Department of Biostatistics and Informatics (S.M.L., G.L.K., K.A.Y., J.E.H., L.M.D.), University of Colorado Anschutz Medical Campus, Aurora
| | - Gregory L Kinney
- Department of Biostatistics and Informatics (S.M.L., G.L.K., K.A.Y., J.E.H., L.M.D.), University of Colorado Anschutz Medical Campus, Aurora
| | - Kendra A Young
- Department of Biostatistics and Informatics (S.M.L., G.L.K., K.A.Y., J.E.H., L.M.D.), University of Colorado Anschutz Medical Campus, Aurora
| | - John E Hokanson
- Department of Biostatistics and Informatics (S.M.L., G.L.K., K.A.Y., J.E.H., L.M.D.), University of Colorado Anschutz Medical Campus, Aurora
| | - R Graham Barr
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY (R.G.B.)
| | - Robert Steiner
- Department of Thoracic Medicine and Surgery and Department of Radiology, Temple University Health System, Philadelphia, PA (R.S.)
| | - Hrudaya Nath
- Department of Medicine, University of Alabama at Birmingham (H.N.)
| | - Carmen Lopez-Garcia
- Department of Medicine, Los Angeles Biomedical Research Institute, Torrance, CA (M.J.B., C.L.-G., S.R., K.O., D.L., R.C.)
| | - Lindsey M Duca
- Department of Epidemiology (S.M.L., L.M.D., E.A.R.), University of Colorado Anschutz Medical Campus, Aurora.,Department of Biostatistics and Informatics (S.M.L., G.L.K., K.A.Y., J.E.H., L.M.D.), University of Colorado Anschutz Medical Campus, Aurora
| | - Sina Rahmani
- Department of Medicine, Los Angeles Biomedical Research Institute, Torrance, CA (M.J.B., C.L.-G., S.R., K.O., D.L., R.C.)
| | - Kazuhiro Osawa
- Department of Medicine, Los Angeles Biomedical Research Institute, Torrance, CA (M.J.B., C.L.-G., S.R., K.O., D.L., R.C.)
| | - Elizabeth A Regan
- Department of Epidemiology (S.M.L., L.M.D., E.A.R.), University of Colorado Anschutz Medical Campus, Aurora.,Department of Medicine, National Jewish Health, Denver, CO (E.A.R.)
| | - Dong Li
- Department of Medicine, Los Angeles Biomedical Research Institute, Torrance, CA (M.J.B., C.L.-G., S.R., K.O., D.L., R.C.)
| | - Richard Casaburi
- Department of Medicine, Los Angeles Biomedical Research Institute, Torrance, CA (M.J.B., C.L.-G., S.R., K.O., D.L., R.C.)
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46
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Washko GR, Nardelli P, Ash SY, Vegas Sanchez-Ferrero G, Rahaghi FN, Come CE, Dransfield MT, Kalhan R, Han MK, Bhatt SP, Wells JM, Aaron CP, Diaz AA, Ross JC, Cuttica MJ, Labaki WW, Querejeta Roca G, Shah AM, Young K, Kinney GL, Hokanson JE, Agustí A. Arterial Vascular Pruning, Right Ventricular Size, and Clinical Outcomes in Chronic Obstructive Pulmonary Disease. A Longitudinal Observational Study. Am J Respir Crit Care Med 2019; 200:454-461. [PMID: 30758975 PMCID: PMC6701031 DOI: 10.1164/rccm.201811-2063oc] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/08/2019] [Indexed: 01/05/2023] Open
Abstract
Rationale: Cor pulmonale (right ventricular [RV] dilation) and cor pulmonale parvus (RV shrinkage) are both described in chronic obstructive pulmonary disease (COPD). The identification of emphysema as a shared risk factor suggests that additional disease characterization is needed to understand these widely divergent cardiac processes.Objectives: To explore the relationship between computed tomography measures of emphysema and distal pulmonary arterial morphology with RV volume, and their association with exercise capacity and mortality in ever-smokers with COPD enrolled in the COPDGene Study.Methods: Epicardial (myocardium and chamber) RV volume (RVEV), distal pulmonary arterial blood vessel volume (arterial BV5: vessels <5 mm2 in cross-section), and objective measures of emphysema were extracted from 3,506 COPDGene computed tomography scans. Multivariable linear and Cox regression models and the log-rank test were used to explore the association between emphysema, arterial BV5, and RVEV with exercise capacity (6-min-walk distance) and all-cause mortality.Measurements and Main Results: The RVEV was approximately 10% smaller in Global Initiative for Chronic Obstructive Lung Disease stage 4 versus stage 1 COPD (P < 0.0001). In multivariable modeling, a 10-ml decrease in arterial BV5 (pruning) was associated with a 1-ml increase in RVEV. For a given amount of emphysema, relative preservation of the arterial BV5 was associated with a smaller RVEV. An increased RVEV was associated with reduced 6-minute-walk distance and in those with arterial pruning an increased mortality.Conclusions: Pulmonary arterial pruning is associated with clinically significant increases in RV volume in smokers with COPD and is related to exercise capacity and mortality in COPD.Clinical trial registered with www.clinicaltrials.gov (NCT00608764).
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Affiliation(s)
| | | | - Samuel Y. Ash
- Division of Pulmonary and Critical Care, Department of Medicine
| | | | | | - Carolyn E. Come
- Division of Pulmonary and Critical Care, Department of Medicine
| | - Mark T. Dransfield
- Lung Health Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Ravi Kalhan
- Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - MeiLan K. Han
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Surya P. Bhatt
- Lung Health Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - J. Michael Wells
- Lung Health Center, University of Alabama at Birmingham, Birmingham, Alabama
| | | | | | - James C. Ross
- Applied Chest Imaging Laboratory, Department of Radiology
| | - Michael J. Cuttica
- Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Wassim W. Labaki
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | | | - Amil M. Shah
- Division of Cardiovascular, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Kendra Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado; and
| | - Gregory L. Kinney
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado; and
| | - John E. Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado; and
| | | | - for the COPDGene Investigators
- Division of Pulmonary and Critical Care, Department of Medicine
- Applied Chest Imaging Laboratory, Department of Radiology
- Department of Anesthesia, and
- Division of Cardiovascular, Brigham and Women’s Hospital, Boston, Massachusetts
- Lung Health Center, University of Alabama at Birmingham, Birmingham, Alabama
- Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado; and
- Hospital Clinic Barcelona, Barcelona, Spain
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47
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Kanter JE, Shao B, Kramer F, Barnhart S, Shimizu-Albergine M, Vaisar T, Graham MJ, Crooke RM, Manuel CR, Haeusler RA, Mar D, Bomsztyk K, Hokanson JE, Kinney GL, Snell-Bergeon JK, Heinecke JW, Bornfeldt KE. Increased apolipoprotein C3 drives cardiovascular risk in type 1 diabetes. J Clin Invest 2019; 129:4165-4179. [PMID: 31295146 DOI: 10.1172/jci127308] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Type 1 diabetes mellitus (T1DM) increases the risk of atherosclerotic cardiovascular disease (CVD) in humans by poorly understood mechanisms. Using mouse models of T1DM-accelerated atherosclerosis, we found that relative insulin deficiency rather than hyperglycemia elevated levels of apolipoprotein C3 (APOC3), an apolipoprotein that prevents clearance of triglyceride-rich lipoproteins (TRLs) and their remnants. We then showed that serum APOC3 levels predict incident CVD events in subjects with T1DM in the Coronary Artery Calcification in Type 1 Diabetes (CACTI) study. To explore underlying mechanisms, we investigated the impact of Apoc3 antisense oligonucleotides (ASOs) on lipoprotein metabolism and atherosclerosis in a mouse model of T1DM. Apoc3 ASO treatment abolished the increased hepatic Apoc3 expression in diabetic mice - resulting in lower levels of TRLs - without improving glycemic control. APOC3 suppression also prevented arterial accumulation of APOC3-containing lipoprotein particles, macrophage foam cell formation, and the accelerated atherosclerosis in diabetic mice. Our observations demonstrate that relative insulin deficiency increases APOC3 and that this results in elevated levels of TRLs and accelerated atherosclerosis in a mouse model of T1DM. Because serum levels of APOC3 predicted incident CVD events in the CACTI study, inhibiting APOC3 might reduce CVD risk in T1DM patients.
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Affiliation(s)
- Jenny E Kanter
- Department of Medicine, UW Medicine Diabetes Institute, University of Washington, Seattle, Washington, USA
| | - Baohai Shao
- Department of Medicine, UW Medicine Diabetes Institute, University of Washington, Seattle, Washington, USA
| | - Farah Kramer
- Department of Medicine, UW Medicine Diabetes Institute, University of Washington, Seattle, Washington, USA
| | - Shelley Barnhart
- Department of Medicine, UW Medicine Diabetes Institute, University of Washington, Seattle, Washington, USA
| | - Masami Shimizu-Albergine
- Department of Medicine, UW Medicine Diabetes Institute, University of Washington, Seattle, Washington, USA
| | - Tomas Vaisar
- Department of Medicine, UW Medicine Diabetes Institute, University of Washington, Seattle, Washington, USA
| | | | | | - Clarence R Manuel
- Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | - Rebecca A Haeusler
- Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | - Daniel Mar
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, USA
| | - Karol Bomsztyk
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, Washington, USA
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, USA
| | - Gregory L Kinney
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, USA
| | - Janet K Snell-Bergeon
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Jay W Heinecke
- Department of Medicine, UW Medicine Diabetes Institute, University of Washington, Seattle, Washington, USA
| | - Karin E Bornfeldt
- Department of Medicine, UW Medicine Diabetes Institute, University of Washington, Seattle, Washington, USA.,Department of Pathology, University of Washington, Seattle, Washington, USA
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48
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Chen J, Cho M, Silverman EK, Hokanson JE, Kinney GL, Crapo JD, Rennard S, Dy J, Castaldi P. Turning subtypes into disease axes to improve prediction of COPD progression. Thorax 2019; 74:906-909. [PMID: 31189730 DOI: 10.1136/thoraxjnl-2018-213005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/06/2019] [Accepted: 05/13/2019] [Indexed: 11/04/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is an umbrella definition encompassing multiple disease processes. COPD heterogeneity has been described as distinct subgroups of individuals (subtypes) or as continuous measures of COPD variability (disease axes). There is little consensus on whether subtypes or disease axes are preferred, and the relative value of disease axes and subtypes for predicting COPD progression is unknown. Using a propensity score approach to learn disease axes from pairs of subtypes, we demonstrate that these disease axes predict prospective forced expiratory volume in 1 s decline and emphysema progression more accurately than the subtype pairs from which they were derived.
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Affiliation(s)
- Junxiang Chen
- Department of Electrical and Computer Engineering, Northeastern University, Boston, United States
| | - Michael Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, United States.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, United States
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, United States.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, United States
| | - John E Hokanson
- Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, USA
| | - Greg L Kinney
- Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, USA
| | - James D Crapo
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Stephen Rennard
- Division of Pulmonary, Critical Care, Sleep and Allergy, University of Nebraska Medical Center, Omaha, United States.,IMED Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Jennifer Dy
- Department of Electrical and Computer Engineering, Northeastern University, Boston, United States
| | - Peter Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, United States .,Division of Primary Care and Internal Medicone, Brigham and Women's Hospital, Boston, United States
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49
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Shrine N, Guyatt AL, Erzurumluoglu AM, Jackson VE, Hobbs BD, Melbourne CA, Batini C, Fawcett KA, Song K, Sakornsakolpat P, Li X, Boxall R, Reeve NF, Obeidat M, Zhao JH, Wielscher M, Weiss S, Kentistou KA, Cook JP, Sun BB, Zhou J, Hui J, Karrasch S, Imboden M, Harris SE, Marten J, Enroth S, Kerr SM, Surakka I, Vitart V, Lehtimäki T, Allen RJ, Bakke PS, Beaty TH, Bleecker ER, Bossé Y, Brandsma CA, Chen Z, Crapo JD, Danesh J, DeMeo DL, Dudbridge F, Ewert R, Gieger C, Gulsvik A, Hansell AL, Hao K, Hoffman JD, Hokanson JE, Homuth G, Joshi PK, Joubert P, Langenberg C, Li X, Li L, Lin K, Lind L, Locantore N, Luan J, Mahajan A, Maranville JC, Murray A, Nickle DC, Packer R, Parker MM, Paynton ML, Porteous DJ, Prokopenko D, Qiao D, Rawal R, Runz H, Sayers I, Sin DD, Smith BH, Artigas MS, Sparrow D, Tal-Singer R, Timmers PRHJ, Van den Berge M, Whittaker JC, Woodruff PG, Yerges-Armstrong LM, Troyanskaya OG, Raitakari OT, Kähönen M, Polašek O, Gyllensten U, Rudan I, Deary IJ, Probst-Hensch NM, Schulz H, James AL, Wilson JF, Stubbe B, Zeggini E, Jarvelin MR, Wareham N, Silverman EK, Hayward C, Morris AP, Butterworth AS, Scott RA, Walters RG, Meyers DA, Cho MH, Strachan DP, Hall IP, Tobin MD, Wain LV. Author Correction: New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries. Nat Genet 2019; 51:1067. [PMID: 31110354 DOI: 10.1038/s41588-019-0438-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anna L Guyatt
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Victoria E Jackson
- Department of Health Sciences, University of Leicester, Leicester, UK.,Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Kijoung Song
- Target Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | - Phuwanat Sakornsakolpat
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Xingnan Li
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Ruth Boxall
- Nuffield Department of Population Health, University of Oxford, Oxford, UK.,Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Nicola F Reeve
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Jing Hua Zhao
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health,Imperial College London, London, UK
| | | | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Katherine A Kentistou
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.,Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - James P Cook
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Benjamin B Sun
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jian Zhou
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Jennie Hui
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.,School of Population Health, The University of Western Australia, Crawley, Western Australia, Australia.,PathWest Laboratory Medicine of WA,Sir Charles Gairdner Hospital, Crawley, Western Australia, Australia.,School of Pathology and Laboratory Medicine, The University of Western Australia, Crawley, Western Australia, Australia
| | - Stefan Karrasch
- Institute of Epidemiology, Helmholtz Zentrum Muenchen-German Research Center for Environmental Health, Neuherberg, Germany.,Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.,Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Stefan Enroth
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden
| | - Shona M Kerr
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ida Surakka
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,The National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Richard J Allen
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Per S Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins University School of Public Health, Baltimore, MD, USA
| | - Eugene R Bleecker
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Québec, Canada.,Institut Universitaire de Cardiologie et de Pneumologie de Québec,Laval University, Québec, Canada
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, GRIAC Research Institute,University of Groningen, Groningen, The Netherlands
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - James D Crapo
- National Jewish Health, Denver, CO, USA.,Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - John Danesh
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine,Addenbrooke's Hospital, Cambridge, UK.,Department of Human Genetics, Wellcome Trust Sanger Institute, Cambridge, UK.,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ralf Ewert
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Anna L Hansell
- Centre for Environmental Health & Sustainability, University of Leicester, Leicester, UK.,UK Small Area Health Statistics Unit, MRC-PHE Centre for Environment and Health, School of Public Health,Imperial College London, London, UK.,Imperial College Healthcare NHS Trust,St Mary's Hospital, London, UK
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec,Laval University, Québec, Canada.,Department of Molecular Biology, Medical Biochemistry, and Pathology,Laval University, Québec, Canada
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Xuan Li
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Liming Li
- Department of Epidemiology & Biostatistics, Peking University Health Science Center, Beijing, China
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Lars Lind
- Department of Medical Sciences, Cardiovascular Epidemiology,Uppsala University, Uppsala, Sweden
| | | | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Alison Murray
- The Institute of Medical Sciences, Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, UK
| | - David C Nickle
- MRL, Merck & Co., Inc, Kenilworth, NJ, USA.,Gossamer Bio, San Diego, CA, USA
| | - Richard Packer
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Megan L Paynton
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - David J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.,Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Heiko Runz
- MRL, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Ian Sayers
- Division of Respiratory Medicine and NIHR-Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Don D Sin
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada.,Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - María Soler Artigas
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Barcelona, Spain
| | - David Sparrow
- VA Boston Healthcare System, Boston, MA, USA.,Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | | | - Paul R H J Timmers
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Maarten Van den Berge
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, GRIAC Research Institute,University of Groningen, Groningen, The Netherlands
| | - John C Whittaker
- Target Sciences - R&D, GSK Medicines Research Centre, Stevenage, UK
| | - Prescott G Woodruff
- UCSF Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
| | | | - Olga G Troyanskaya
- Department of Computer Science, Princeton University, Princeton, NJ, USA.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland.,Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences,University of Tampere, Tampere, Finland
| | - Ozren Polašek
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.,University of Split School of Medicine, Split, Croatia
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.,Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Nicole M Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Holger Schulz
- Institute of Epidemiology, Helmholtz Zentrum Muenchen-German Research Center for Environmental Health, Neuherberg, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Alan L James
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.,Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.,School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia, Australia
| | - James F Wilson
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.,Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Beate Stubbe
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
| | - Eleftheria Zeggini
- Wellcome Sanger Institute, Hinxton, UK.,Institute of Translational Genomics, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health,Imperial College London, London, UK.,Center for Life Course Health Research, Faculty of Medicine,University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland.,Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Nick Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Robert A Scott
- Target Sciences - R&D, GSK Medicines Research Centre, Stevenage, UK
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Deborah A Meyers
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, UK
| | - Ian P Hall
- Division of Respiratory Medicine and NIHR-Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK. .,National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK. .,National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
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Pirim D, Radwan ZH, Wang X, Niemsiri V, Hokanson JE, Hamman RF, Feingold E, Bunker CH, Demirci FY, Kamboh MI. Apolipoprotein E-C1-C4-C2 gene cluster region and inter-individual variation in plasma lipoprotein levels: a comprehensive genetic association study in two ethnic groups. PLoS One 2019; 14:e0214060. [PMID: 30913229 PMCID: PMC6435132 DOI: 10.1371/journal.pone.0214060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 10/18/2018] [Accepted: 02/12/2019] [Indexed: 01/15/2023] Open
Abstract
The apolipoprotein E-C1-C4-C2 gene cluster at 19q13.32 encodes four amphipathic apolipoproteins. The influence of APOE common polymorphisms on plasma lipid/lipoprotein profile, especially on LDL-related traits, is well recognized; however, little is known about the role of other genes/variants in this gene cluster. In this study, we evaluated the role of common and uncommon/rare genetic variation in this gene region on inter-individual variation in plasma lipoprotein levels in non-Hispanic Whites (NHWs) and African blacks (ABs). In the variant discovery step, the APOE, APOC1, APOC4, APOC2 genes were sequenced along with their flanking and hepatic control regions (HCR1 and HCR2) in 190 subjects with extreme HDL-C/TG levels. The next step involved the genotyping of 623 NHWs and 788 ABs for the identified uncommon/rare variants and common tagSNPs along with additional relevant SNPs selected from public resources, followed by association analyses with lipid traits. A total of 230 sequence variants, including 15 indels were identified, of which 65 were novel. A total of 70 QC-passed variants in NHWs and 108 QC-passed variants in ABs were included in the final association analyses. Single-site association analysis of SNPs with MAF>1% revealed 20 variants in NHWs and 24 variants in ABs showing evidence of association with at least one lipid trait, including several variants exhibiting independent associations from the established APOE polymorphism even after multiple-testing correction. Overall, our study has confirmed known associations and also identified novel associations in this genomic region with various lipid traits. Our data also support the contribution of both common and uncommon/rare variation in this gene region in affecting plasma lipid profile in the general population.
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Affiliation(s)
- Dilek Pirim
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Molecular Biology and Genetics, Faculty of Arts&Science, Uludag University, Gorukle, Bursa, Turkey
| | - Zaheda H. Radwan
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Xingbin Wang
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Vipavee Niemsiri
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - John E. Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Richard F. Hamman
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Clareann H. Bunker
- Department of Epidemiology, Graduate School of Public Health, University Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - F. Yesim Demirci
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (MIK); (FYD)
| | - M. Ilyas Kamboh
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (MIK); (FYD)
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