Polygenic transcriptome risk scores for COPD and lung function improve cross-ethnic portability of prediction in the NHLBI TOPMed program.

Humans Lung National Heart, Lung, and Blood Institute (U.S.) Pulmonary Disease, Chronic Obstructive / genetics Risk Factors Transcriptome United States / epidemiology
cross-ethnic portability gene expression integrative analysis polygenic transcriptome risk score pulmonary disease risk prediction

Journal

American journal of human genetics
ISSN: 1537-6605
Titre abrégé: Am J Hum Genet
Pays: United States
ID NLM: 0370475

Informations de publication

Date de publication:
05 05 2022
Historique:
received: 05 11 2021
accepted: 04 03 2022
pubmed: 7 4 2022
medline: 11 5 2022
entrez: 6 4 2022
Statut: ppublish

Résumé

While polygenic risk scores (PRSs) enable early identification of genetic risk for chronic obstructive pulmonary disease (COPD), predictive performance is limited when the discovery and target populations are not well matched. Hypothesizing that the biological mechanisms of disease are shared across ancestry groups, we introduce a PrediXcan-derived polygenic transcriptome risk score (PTRS) to improve cross-ethnic portability of risk prediction. We constructed the PTRS using summary statistics from application of PrediXcan on large-scale GWASs of lung function (forced expiratory volume in 1 s [FEV

Identifiants

DOI: 10.1016/j.ajhg.2022.03.007 PMID: 35385699 PMC: PMC9118106
pubmed: 35385699
pii: S0002-9297(22)00103-3
doi: 10.1016/j.ajhg.2022.03.007
pmc: PMC9118106
pii:
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural

Langues

eng

Sous-ensembles de citation

IM

Pagination

857-870

Subventions

Organisme : Medical Research Council
ID : MC_PC_17228
Pays : United Kingdom
Organisme : NHLBI NIH HHS
ID : R01 HL105756
Pays : United States
Organisme : NHGRI NIH HHS
ID : R15 HG009569
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL137927
Pays : United States
Organisme : NHLBI NIH HHS
ID : K01 HL129039
Pays : United States
Organisme : NHLBI NIH HHS
ID : R03 HL154284
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL131565
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL122477
Pays : United States
Organisme : NIDDK NIH HHS
ID : P30 DK020595
Pays : United States
Organisme : Medical Research Council
ID : MC_QA137853
Pays : United Kingdom
Organisme : NHLBI NIH HHS
ID : R01 HL153248
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL153805
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL147148
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL089856
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL135142
Pays : United States
Organisme : NHLBI NIH HHS
ID : R35 HL135818
Pays : United States

Informations de copyright

Copyright © 2022 American Society of Human Genetics. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests In the past three years, E.K.S. and M.H.C. have received institutional grant support from GlaxoSmithKline and Bayer. M.H.C. has received consulting and speaking fees from Illumina and AstraZeneca. B.M.P. serves on the Steering Committee of the Yale Open Data Access project funded by Johnson & Johnson. T.L. is an advisor for Variant Bio, Goldfinch Bio, and GSK. T.L. also has stock in Variant Bio. All other authors have declared no competing interests.

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Auteurs

Xiaowei Hu (X)

Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA.

Dandi Qiao (D)

Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.

Wonji Kim (W)

Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.

Matthew Moll (M)

Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.

Pallavi P Balte (PP)

Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY 10032, USA.

Leslie A Lange (LA)

Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine Anschutz Medical Campus, Aurora, CO 80045, USA.

Traci M Bartz (TM)

Department of Biostatistics, University of Washington, Seattle, WA 98195, USA; Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA.

Rajesh Kumar (R)

Division of Allergy and Clinical Immunology, Ann and Robert H. Lurie Children's Hospital, Chicago, IL 60611, USA; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.

Xingnan Li (X)

Department of Medicine, University of Arizona, Tucson, AZ 85724, USA.

Bing Yu (B)

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 77030, USA.

Brian E Cade (BE)

Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA.

Cecelia A Laurie (CA)

Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.

Tamar Sofer (T)

Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA.

Ingo Ruczinski (I)

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.

Deborah A Nickerson (DA)

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.

Donna M Muzny (DM)

The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

Ginger A Metcalf (GA)

The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

Harshavardhan Doddapaneni (H)

The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

Stacy Gabriel (S)

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

Namrata Gupta (N)

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

Shannon Dugan-Perez (S)

The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

L Adrienne Cupples (LA)

Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA.

Laura R Loehr (LR)

Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.

Deepti Jain (D)

Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.

Jerome I Rotter (JI)

The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA.

James G Wilson (JG)

Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115, USA.

Bruce M Psaty (BM)

Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA 98101, USA.

Myriam Fornage (M)

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 77030, USA; Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.

Alanna C Morrison (AC)

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 77030, USA.

Ramachandran S Vasan (RS)

Boston University and the National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA 01702, USA; Department of Preventive Medicine and Epidemiology, School of Medicine and Public Health, Boston University, Boston, MA 02118, USA.

George Washko (G)

Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.

Stephen S Rich (SS)

Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA.

George T O'Connor (GT)

Pulmonary Center, Boston University, School of Medicine, Boston, MA 02118, USA.

Eugene Bleecker (E)

Department of Medicine, University of Arizona, Tucson, AZ 85724, USA.

Robert C Kaplan (RC)

Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

Ravi Kalhan (R)

Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.

Susan Redline (S)

Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA.

Sina A Gharib (SA)

Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA 98109, USA.

Deborah Meyers (D)

Department of Medicine, University of Arizona, Tucson, AZ 85724, USA.

Victor Ortega (V)

Pulmonary and Critical Care, School of Medicine, Wake Forest University, Winston-Salem, NC 27157, USA.

Josée Dupuis (J)

Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA.

Stephanie J London (SJ)

Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Durham, NC 27709, USA.

Tuuli Lappalainen (T)

New York Genome Center, New York, NY 10013, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA.

Elizabeth C Oelsner (EC)

Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY 10032, USA.

Edwin K Silverman (EK)

Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.

R Graham Barr (RG)

Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY 10032, USA.

Timothy A Thornton (TA)

Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.

Heather E Wheeler (HE)

Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA.

Michael H Cho (MH)

Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.

Hae Kyung Im (HK)

Section of Genetic Medicine, The University of Chicago, Chicago, IL 60637, USA.

Ani Manichaikul (A)

Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA. Electronic address: am3xa@virginia.edu.

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