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Harnessing functional annotation to improve the accuracy and transferability of polygenic scores

Polygenic scores (PGS) have shown promise in predicting complex traits and disease risk, but their accuracy remains limited and poorly transferable across ancestries. Integrating functional annotations with whole-genome sequencing data can improve prediction by prioritizing likely causal variants shared across populations and by assigning greater weight to variants in biologically relevant regions.

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References

  1. Ding, Y. et al. Polygenic scoring accuracy varies across the genetic ancestry continuum. Nature 618, 774–781 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Wray, N. R. et al. From basic science to clinical application of polygenic risk scores: a primer. JAMA Psychiatry 78, 101–109 (2021).

    Article  PubMed  Google Scholar 

  3. Hou, K. et al. Causal effects on complex traits are similar for common variants across segments of different continental ancestries within admixed individuals. Nat. Genet. 55, 549–558 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Hu, S. et al. Fine-scale population structure and widespread conservation of genetic effect sizes between human groups across traits. Nat. Genet. 57, 379–389 (2025).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Goddard, M. E., Wray, N. R., Verbyla, K. & Visscher, P. M. Estimating effects and making predictions from genome-wide marker data. Stat. Sci. 24, 517–529 (2009).

    Article  Google Scholar 

  6. Zheng, Z. et al. Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries. Nat. Genet. 56, 767–777 (2024).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Yang, Z. et al. CARMA is a new Bayesian model for fine-mapping in genome-wide association meta-analyses. Nat. Genet. 55, 1057–1065 (2023).

    Article  CAS  PubMed  Google Scholar 

  8. Li, X. et al. Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale. Nat. Genet. 52, 969–983 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Barbadilla-Martínez, L. et al. Predicting gene expression from DNA sequence using deep learning models. Nat. Rev. Genet. https://doi.org/10.1038/s41576-025-00841-2 (2025).

    Article  PubMed  Google Scholar 

  10. Weissbrod, O. et al. Leveraging fine-mapping and multipopulation training data to improve cross-population polygenic risk scores. Nat. Genet. 54, 450–458 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Correspondence to Peter M. Visscher.

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Zeng, J., Visscher, P.M. Harnessing functional annotation to improve the accuracy and transferability of polygenic scores. Nat Rev Genet (2025). https://doi.org/10.1038/s41576-025-00893-4

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