MUSSEL: Enhanced Bayesian polygenic risk prediction leveraging information across multiple ancestry groups.

Bayesian hierarchical modeling effect-size distribution ensemble learning genome-wide association studies multi-ancestry polygenic prediction polygenic architecture

Journal

Cell genomics
ISSN: 2666-979X
Titre abrégé: Cell Genom
Pays: United States
ID NLM: 9918284260106676

Informations de publication

Date de publication:
10 Apr 2024
Historique:
received: 23 03 2023
revised: 07 09 2023
accepted: 14 03 2024
medline: 12 4 2024
pubmed: 12 4 2024
entrez: 11 4 2024
Statut: ppublish

Résumé

Polygenic risk scores (PRSs) are now showing promising predictive performance on a wide variety of complex traits and diseases, but there exists a substantial performance gap across populations. We propose MUSSEL, a method for ancestry-specific polygenic prediction that borrows information in summary statistics from genome-wide association studies (GWASs) across multiple ancestry groups via Bayesian hierarchical modeling and ensemble learning. In our simulation studies and data analyses across four distinct studies, totaling 5.7 million participants with a substantial ancestral diversity, MUSSEL shows promising performance compared to alternatives. For example, MUSSEL has an average gain in prediction R

Identifiants

DOI: 10.1016/j.xgen.2024.100539 PMID: 38604127
pubmed: 38604127
pii: S2666-979X(24)00095-8
doi: 10.1016/j.xgen.2024.100539
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

100539

Investigateurs

Stella Aslibekyan (S)
Adam Auton (A)
Elizabeth Babalola (E)
Robert K Bell (RK)
Jessica Bielenberg (J)
Katarzyna Bryc (K)
Emily Bullis (E)
Daniella Coker (D)
Gabriel Cuellar Partida (G)
Devika Dhamija (D)
Sayantan Das (S)
Sarah L Elson (SL)
Nicholas Eriksson (N)
Teresa Filshtein (T)
Alison Fitch (A)
Kipper Fletez-Brant (K)
Pierre Fontanillas (P)
Will Freyman (W)
Julie M Granka (JM)
Karl Heilbron (K)
Alejandro Hernandez (A)
Barry Hicks (B)
David A Hinds (DA)
Ethan M Jewett (EM)
Yunxuan Jiang (Y)
Katelyn Kukar (K)
Alan Kwong (A)
Keng-Han Lin (KH)
Bianca A Llamas (BA)
Maya Lowe (M)
Jey C McCreight (JC)
Matthew H McIntyre (MH)
Steven J Micheletti (SJ)
Meghan E Moreno (ME)
Priyanka Nandakumar (P)
Dominique T Nguyen (DT)
Elizabeth S Noblin (ES)
Jared O'Connell (J)
Aaron A Petrakovitz (AA)
G David Poznik (GD)
Alexandra Reynoso (A)
Morgan Schumacher (M)
Anjali J Shastri (AJ)
Janie F Shelton (JF)
Jingchunzi Shi (J)
Suyash Shringarpure (S)
Qiaojuan Jane Su (QJ)
Susana A Tat (SA)
Christophe Toukam Tchakouté (CT)
Vinh Tran (V)
Joyce Y Tung (JY)
Xin Wang (X)
Wei Wang (W)
Catherine H Weldon (CH)
Peter Wilton (P)
Corinna D Wong (CD)

Informations de copyright

Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests J. Zhan, Y.J., J.O., and B.L.K. are employed by and hold stock or stock options in 23andMe, Inc.

Auteurs

Jin Jin (J)

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19103, USA. Electronic address: jin.jin@pennmedicine.upenn.edu.

Jianan Zhan (J)

23andMe, Inc., Sunnyvale, CA 94086, USA.

Jingning Zhang (J)

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

Ruzhang Zhao (R)

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

Jared O'Connell (J)

23andMe, Inc., Sunnyvale, CA 94086, USA.

Yunxuan Jiang (Y)

23andMe, Inc., Sunnyvale, CA 94086, USA.
23andMe, Inc., Sunnyvale, CA 94086, USA.

Steven Buyske (S)

Department of Statistics, Rutgers University, New Brunswick, NJ 08854, USA.

Christopher Gignoux (C)

Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.

Christopher Haiman (C)

Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032, USA.

Eimear E Kenny (EE)

Icahn Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

Charles Kooperberg (C)

Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.

Kari North (K)

Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA.

Bertram L Koelsch (BL)

23andMe, Inc., Sunnyvale, CA 94086, USA.

Genevieve Wojcik (G)

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

Haoyu Zhang (H)

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.

Nilanjan Chatterjee (N)

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA. Electronic address: nilanjan@jhu.edu.

Classifications MeSH