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一种强大的跨血统多基因风险评分方法。

: A powerful trans-ancestry Polygenic Risk Score method.

作者信息

Hoggart Clive, Choi Shing Wan, García-González Judit, Souaiaia Tade, Preuss Michael, O'Reilly Paul

出版信息

bioRxiv. 2023 Feb 21:2023.02.17.528938. doi: 10.1101/2023.02.17.528938.

DOI:10.1101/2023.02.17.528938
PMID:36865148
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9979992/
Abstract

Polygenic Risk Scores (PRS) have huge potential to contribute to biomedical research and to a future of precision medicine, but to date their calculation relies largely on Europeanancestry GWAS data. This global bias makes most PRS substantially less accurate in individuals of non-European ancestry. Here we present , a novel Bayesian PRS method that leverages shared genetic effects across ancestries to increase the accuracy of PRS in non-European populations. The performance of is evaluated in simulated data and real UK Biobank (UKB) data across 19 traits in African, South Asian and East Asian ancestry individuals, using both UKB and Biobank Japan GWAS summary statistics. is compared to the leading alternative, , and two single-ancestry PRS methods adapted for trans-ancestry prediction. PRS trained in the UK Biobank are then validated out-of-cohort in the independent Mount Sinai (New York) Bio Biobank. Simulations reveal that performance, relative to , increases as uncertainty increases: with lower heritability, higher polygenicity, greater between-population genetic diversity, and when causal variants are not present in the data. Our simulation results are consistent with real data analyses in which has better predictive accuracy in African ancestry samples, especially in out-of-cohort prediction (into Bio ), which shows a 60% boost in mean compared to ( = 2 10 ). performs the full PRS analysis pipeline, is computationally efficient, and is a powerful method for deriving PRS in diverse and under-represented ancestry populations.

摘要

多基因风险评分(PRS)在生物医学研究和精准医学未来发展中具有巨大潜力,但迄今为止,其计算主要依赖于欧洲血统的全基因组关联研究(GWAS)数据。这种全球偏差使得大多数PRS在非欧洲血统个体中的准确性大幅降低。在此,我们提出了一种新颖的贝叶斯PRS方法,该方法利用不同血统间共享的遗传效应来提高非欧洲人群中PRS的准确性。我们使用英国生物银行(UKB)和日本生物银行GWAS汇总统计数据,在非洲、南亚和东亚血统个体的19个性状的模拟数据和真实UKB数据中评估了该方法的性能。将该方法与领先的替代方法以及两种适用于跨血统预测的单血统PRS方法进行了比较。然后,在独立的西奈山(纽约)生物银行中对在英国生物银行中训练的PRS进行了队列外验证。模拟结果表明,相对于其他方法,随着不确定性增加,该方法的性能会提高:在遗传力较低、多基因性较高、人群间遗传多样性较大以及数据中不存在因果变异时。我们的模拟结果与实际数据分析一致,在实际数据分析中,该方法在非洲血统样本中具有更好的预测准确性,尤其是在队列外预测(进入生物银行)中,与其他方法相比,平均预测准确性提高了60%(P = 2×10⁻⁶)。该方法执行完整的PRS分析流程,计算效率高,是在多样化和代表性不足的血统人群中推导PRS的强大方法。

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引用本文的文献

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Methodologies underpinning polygenic risk scores estimation: a comprehensive overview.多基因风险评分估计的方法学基础:全面综述。
Hum Genet. 2024 Nov;143(11):1265-1280. doi: 10.1007/s00439-024-02710-0. Epub 2024 Oct 19.
2
Exploring the role of underrepresented populations in polygenic risk scores for neurodegenerative disease risk prediction.探索未被充分代表的人群在神经退行性疾病风险预测的多基因风险评分中的作用。
Front Neurosci. 2024 May 27;18:1380860. doi: 10.3389/fnins.2024.1380860. eCollection 2024.