1. Integrative polygenic risk score improves the prediction accuracy of complex traits and diseases.
- Author
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Truong B, Hull LE, Ruan Y, Huang QQ, Hornsby W, Martin H, van Heel DA, Wang Y, Martin AR, Lee SH, and Natarajan P
- Subjects
- Humans, Multifactorial Inheritance genetics, Genetic Risk Score, Benchmarking, Coronary Artery Disease diagnosis, Manipulation, Osteopathic
- Abstract
Polygenic risk scores (PRSs) are an emerging tool to predict the clinical phenotypes and outcomes of individuals. We propose PRSmix, a framework that leverages the PRS corpus of a target trait to improve prediction accuracy, and PRSmix+, which incorporates genetically correlated traits to better capture the human genetic architecture for 47 and 32 diseases/traits in European and South Asian ancestries, respectively. PRSmix demonstrated a mean prediction accuracy improvement of 1.20-fold (95% confidence interval [CI], [1.10; 1.3]; p = 9.17 × 10
-5 ) and 1.19-fold (95% CI, [1.11; 1.27]; p = 1.92 × 10-6 ), and PRSmix+ improved the prediction accuracy by 1.72-fold (95% CI, [1.40; 2.04]; p = 7.58 × 10-6 ) and 1.42-fold (95% CI, [1.25; 1.59]; p = 8.01 × 10-7 ) in European and South Asian ancestries, respectively. Compared to the previously cross-trait-combination methods with scores from pre-defined correlated traits, we demonstrated that our method improved prediction accuracy for coronary artery disease up to 3.27-fold (95% CI, [2.1; 4.44]; p value after false discovery rate (FDR) correction = 2.6 × 10-4 ). Our method provides a comprehensive framework to benchmark and leverage the combined power of PRS for maximal performance in a desired target population., Competing Interests: Declaration of interests P.N. reports grants from Allelica, Amgen, Apple, Boston Scientific, Genentech, and Novartis; is a consultant to Allelica, Apple, AstraZeneca, Blackstone Life Sciences, Foresite Labs, HeartFlow, Novartis, Genentech, and GV; reports scientific advisory board membership with Esperion Therapeutics, Preciseli, and TenSixteen Bio; is a scientific co-founder of TenSixteen Bio; and reports spousal employment at Vertex Pharmaceuticals, all unrelated to the present work., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)- Published
- 2024
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