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Improving Polygenic Prediction in Ancestrally Diverse Populations

By Yunfeng Ruan, Yen-Feng Lin, Yen-Chen Anne Feng, Chia-Yen Chen, Max Lam, Zhenglin Guo, Stanley Global Asia Initiatives, Lin He, Akira Sawa, Alicia R. Martin, Shengying Qin, Hailiang Huang, Tian Ge

Posted 02 Jan 2021
medRxiv DOI: 10.1101/2020.12.27.20248738

Polygenic risk scores (PRS) have attenuated cross-population predictive performance. As existing genome-wide association studies (GWAS) were predominantly conducted in individuals of European descent, the limited transferability of PRS reduces its clinical value in non-European populations and may exacerbate healthcare disparities. Recent efforts to level ancestry imbalance in genomic research have expanded the scale of non-European GWAS, although most of them remain under-powered. Here we present a novel PRS construction method, PRS-CSx, which improves cross-population polygenic prediction by integrating GWAS summary statistics from multiple populations. PRS-CSx couples genetic effects across populations via a shared continuous shrinkage prior, enabling more accurate effect size estimation by sharing information between summary statistics and leveraging linkage disequilibrium (LD) diversity across discovery samples, while inheriting computational efficiency and robustness from PRS-CS. We show that PRS-CSx outperforms alternative methods across traits with a wide range of genetic architectures, cross-population genetic overlaps and discovery GWAS sample sizes in simulations, and improves the prediction of quantitative traits and schizophrenia risk in non-European populations.

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