Machine learning models for predicting blood pressure phenotypes by combining multiple polygenic risk scores.

Humans Machine Learning Blood Pressure / genetics Multifactorial Inheritance / genetics Phenotype Genome-Wide Association Study / methods Risk Factors Male Female Genetic Predisposition to Disease Models, Genetic Hypertension / genetics Middle Aged Genetic Risk Score

Journal

Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288

Informations de publication

Date de publication:
30 05 2024
Historique:
received: 22 01 2024
accepted: 22 05 2024
medline: 31 5 2024
pubmed: 31 5 2024
entrez: 30 5 2024
Statut: epublish

Résumé

We construct non-linear machine learning (ML) prediction models for systolic and diastolic blood pressure (SBP, DBP) using demographic and clinical variables and polygenic risk scores (PRSs). We developed a two-model ensemble, consisting of a baseline model, where prediction is based on demographic and clinical variables only, and a genetic model, where we also include PRSs. We evaluate the use of a linear versus a non-linear model at both the baseline and the genetic model levels and assess the improvement in performance when incorporating multiple PRSs. We report the ensemble model's performance as percentage variance explained (PVE) on a held-out test dataset. A non-linear baseline model improved the PVEs from 28.1 to 30.1% (SBP) and 14.3% to 17.4% (DBP) compared with a linear baseline model. Including seven PRSs in the genetic model computed based on the largest available GWAS of SBP/DBP improved the genetic model PVE from 4.8 to 5.1% (SBP) and 4.7 to 5% (DBP) compared to using a single PRS. Adding additional 14 PRSs computed based on two independent GWASs further increased the genetic model PVE to 6.3% (SBP) and 5.7% (DBP). PVE differed across self-reported race/ethnicity groups, with primarily all non-White groups benefitting from the inclusion of additional PRSs. In summary, non-linear ML models improves BP prediction in models incorporating diverse populations.

Identifiants

DOI: 10.1038/s41598-024-62945-9 PMID: 38816422
pubmed: 38816422
doi: 10.1038/s41598-024-62945-9
pii: 10.1038/s41598-024-62945-9
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

12436

Subventions

Organisme : NHLBI NIH HHS
ID : R01HL161012
Pays : United States

Informations de copyright

© 2024. The Author(s).

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Auteurs

Yana Hrytsenko (Y)

Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
Department of Medicine, Harvard Medical School, Boston, MA, USA.
CardioVascular Institute (CVI), Beth Israel Deaconess Medical Center, Boston, MA, USA.

Benjamin Shea (B)

CardioVascular Institute (CVI), Beth Israel Deaconess Medical Center, Boston, MA, USA.

Michael Elgart (M)

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

Nuzulul Kurniansyah (N)

Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.

Genevieve Lyons (G)

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

Alanna C Morrison (AC)

Department of Epidemiology, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX, USA.

April P Carson (AP)

Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA.

Bernhard Haring (B)

Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA.
Department of Medicine III, Saarland University, Homburg, Saarland, Germany.

Braxton D Mitchell (BD)

Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.

Bruce M Psaty (BM)

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

Byron C Jaeger (BC)

Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, NC, USA.

C Charles Gu (CC)

The Center for Biostatistics and Data Science, Washington University, St. Louis, USA.

Charles Kooperberg (C)

Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA.

Daniel Levy (D)

The Population Sciences Branch of the National Heart, Lung and Blood Institute, Bethesda, MD, USA.
The Framingham Heart Study, Framingham, MA, USA.

Donald Lloyd-Jones (D)

Department of Preventive Medicine, Northwestern University, Chicago, IL, USA.

Eunhee Choi (E)

Columbia Hypertension Laboratory, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.

Jennifer A Brody (JA)

Department of Medicine, University of Washington, Seattle, WA, USA.
Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA.

Jennifer A Smith (JA)

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.

Jerome I Rotter (JI)

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

Matthew Moll (M)

Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
Department of Medicine, Harvard Medical School, Boston, MA, USA.
VA Boston Healthcare System, West Roxbury, MA, USA.
Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA.

Myriam Fornage (M)

Department of Epidemiology, School of Public Health, Human Genetics Center, 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.

Noah Simon (N)

Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA.

Peter Castaldi (P)

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

Ramon Casanova (R)

Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, NC, USA.

Ren-Hua Chung (RH)

Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Taipei City, Taiwan.

Robert Kaplan (R)

Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA.
Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA.

Ruth J F Loos (RJF)

The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty for Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

Sharon L R Kardia (SLR)

Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA.

Stephen S Rich (SS)

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

Susan Redline (S)

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

Tanika Kelly (T)

Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA.

Timothy O'Connor (T)

Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
Program in Health Equity and Population Health, University of Maryland School of Medicine, Baltimore, MD, USA.

Wei Zhao (W)

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.

Wonji Kim (W)

Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, USA.

Xiuqing Guo (X)

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

Yii-Der Ida Chen (YD)

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

Tamar Sofer (T)

Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA. tsofer@bidmc.harvard.edu.
Department of Medicine, Harvard Medical School, Boston, MA, USA. tsofer@bidmc.harvard.edu.
CardioVascular Institute (CVI), Beth Israel Deaconess Medical Center, Boston, MA, USA. tsofer@bidmc.harvard.edu.
Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA. tsofer@bidmc.harvard.edu.
Center for Life Sciences CLS-934, 3 Blackfan St., Boston, MA, 02115, USA. tsofer@bidmc.harvard.edu.

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