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Urbut SM, Koyama S, Hornsby W, Bhukar R, Kheterpal S, Truong B, Selvaraj MS, Neale B, O’Donnell CJ, Peloso GM, Natarajan P. Bayesian multivariate genetic analysis improves translational insights. iScience 2023; 26:107854. [PMID: 37766997 PMCID: PMC10520309 DOI: 10.1016/j.isci.2023.107854] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/15/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
While lipid traits are known essential mediators of cardiovascular disease, few approaches have taken advantage of their shared genetic effects. We apply a Bayesian multivariate size estimator, mash, to GWAS of four lipid traits in the Million Veterans Program (MVP) and provide posterior mean and local false sign rates for all effects. These estimates borrow information across traits to improve effect size accuracy. We show that controlling local false sign rates accurately and powerfully identifies replicable genetic associations and that multivariate control furthers the ability to explain complex diseases. Our application yields high concordance between independent datasets, more accurately prioritizes causal genes, and significantly improves polygenic prediction beyond state-of-the-art methods by up to 59% for lipid traits. The use of Bayesian multivariate genetic shrinkage has yet to be applied to human quantitative trait GWAS results, and we present a staged approach to prediction on a polygenic scale.
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Affiliation(s)
- Sarah M. Urbut
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - Satoshi Koyama
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Department of Medicine Harvard Medical School, Boston, MA 02115, USA
| | - Whitney Hornsby
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Department of Medicine Harvard Medical School, Boston, MA 02115, USA
| | - Rohan Bhukar
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Department of Medicine Harvard Medical School, Boston, MA 02115, USA
| | - Sumeet Kheterpal
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - Buu Truong
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Department of Medicine Harvard Medical School, Boston, MA 02115, USA
| | - Margaret S. Selvaraj
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Department of Medicine Harvard Medical School, Boston, MA 02115, USA
| | - Benjamin Neale
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Department of Medicine Harvard Medical School, Boston, MA 02115, USA
- Analytic Translational and Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Christopher J. O’Donnell
- Department of Medicine Harvard Medical School, Boston, MA 02115, USA
- VA Boston Department of Veterans Affairs, Boston, MA 02130, USA
| | - Gina M. Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02218, USA
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Department of Medicine Harvard Medical School, Boston, MA 02115, USA
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