Polygenic risk score prediction accuracy convergence

Léo Henches; Jihye Kim; Zhiyu Yang; Simone Rubinacci; Gabriel Pires; Clara Albiñana; Christophe Boetto; Hanna Julienne; Arthur Frouin; Antoine Auvergne; Yuka Suzuki; Sarah Djebali; Olivier Delaneau; Andrea Ganna; Bjarni Vilhjálmsson; Florian Privé; Hugues Aschard

doi:10.1016/j.xhgg.2025.100457

Polygenic risk score prediction accuracy convergence

Léo Henches, Jihye Kim, Zhiyu Yang, Simone Rubinacci, Gabriel Pires, Clara Albiñana, Christophe Boetto, Hanna Julienne, Arthur Frouin, Antoine Auvergne, Yuka Suzuki, Sarah Djebali, Olivier Delaneau, Andrea Ganna, Bjarni Vilhjálmsson, Florian Privé, Hugues Aschard^*

^*Corresponding author for this work

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

Abstract

Polygenic risk scores (PRSs) models trained from genome-wide association study (GWAS) results are set to play a pivotal role in biomedical research addressing multifactorial human diseases. The prospect of using these risk scores in clinical care and public health is generating both enthusiasm and controversy, with varying opinions among experts about their strengths and limitations. The performance of existing polygenic scores is still limited but is expected to improve with increasing GWAS sample sizes and the development of new, more powerful methods. Theoretically, the variance explained by PRS can be as high as the total additive genetic variance, but it is unclear how much of that variance has already been captured by PRS. Here, we conducted a retrospective analysis to assess progress in PRS prediction accuracy since the publication of the first large-scale GWASs, using data from six common human diseases with sufficient GWAS information. We show that although PRS accuracy has grown rapidly over the years, the pace of improvement from recent GWAS has decreased substantially, suggesting that merely increasing GWAS sample sizes may lead to only modest improvements in risk discrimination. We next investigated the factors influencing the maximum achievable prediction using whole-genome sequencing data from 125,000 UK Biobank participants and state-of-the-art modeling of polygenic outcomes. Our analyses suggest that increasing the variant coverage of PRS, using either more imputed variants or sequencing data, is a key component for future improvements in prediction accuracy.

Original language	English
Article number	100457
Journal	Human Genetics and Genomics Advances
Volume	6
Issue	3
ISSN	2666-2477
DOIs	https://doi.org/10.1016/j.xhgg.2025.100457
Publication status	Published - Jul 2025

Keywords

GWAS
polygenic risk prediction
polygenicity
sample size

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Henches, L., Kim, J., Yang, Z., Rubinacci, S., Pires, G., Albiñana, C., Boetto, C., Julienne, H., Frouin, A., Auvergne, A., Suzuki, Y., Djebali, S., Delaneau, O., Ganna, A., Vilhjálmsson, B., Privé, F., & Aschard, H. (2025). Polygenic risk score prediction accuracy convergence. Human Genetics and Genomics Advances, 6(3), Article 100457. https://doi.org/10.1016/j.xhgg.2025.100457

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abstract = "Polygenic risk scores (PRSs) models trained from genome-wide association study (GWAS) results are set to play a pivotal role in biomedical research addressing multifactorial human diseases. The prospect of using these risk scores in clinical care and public health is generating both enthusiasm and controversy, with varying opinions among experts about their strengths and limitations. The performance of existing polygenic scores is still limited but is expected to improve with increasing GWAS sample sizes and the development of new, more powerful methods. Theoretically, the variance explained by PRS can be as high as the total additive genetic variance, but it is unclear how much of that variance has already been captured by PRS. Here, we conducted a retrospective analysis to assess progress in PRS prediction accuracy since the publication of the first large-scale GWASs, using data from six common human diseases with sufficient GWAS information. We show that although PRS accuracy has grown rapidly over the years, the pace of improvement from recent GWAS has decreased substantially, suggesting that merely increasing GWAS sample sizes may lead to only modest improvements in risk discrimination. We next investigated the factors influencing the maximum achievable prediction using whole-genome sequencing data from 125,000 UK Biobank participants and state-of-the-art modeling of polygenic outcomes. Our analyses suggest that increasing the variant coverage of PRS, using either more imputed variants or sequencing data, is a key component for future improvements in prediction accuracy.",

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doi = "10.1016/j.xhgg.2025.100457",

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AU - Henches, Léo

AU - Kim, Jihye

AU - Yang, Zhiyu

AU - Rubinacci, Simone

AU - Pires, Gabriel

AU - Albiñana, Clara

AU - Boetto, Christophe

AU - Julienne, Hanna

AU - Frouin, Arthur

AU - Auvergne, Antoine

AU - Suzuki, Yuka

AU - Djebali, Sarah

AU - Delaneau, Olivier

AU - Ganna, Andrea

AU - Vilhjálmsson, Bjarni

AU - Privé, Florian

AU - Aschard, Hugues

PY - 2025/7

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N2 - Polygenic risk scores (PRSs) models trained from genome-wide association study (GWAS) results are set to play a pivotal role in biomedical research addressing multifactorial human diseases. The prospect of using these risk scores in clinical care and public health is generating both enthusiasm and controversy, with varying opinions among experts about their strengths and limitations. The performance of existing polygenic scores is still limited but is expected to improve with increasing GWAS sample sizes and the development of new, more powerful methods. Theoretically, the variance explained by PRS can be as high as the total additive genetic variance, but it is unclear how much of that variance has already been captured by PRS. Here, we conducted a retrospective analysis to assess progress in PRS prediction accuracy since the publication of the first large-scale GWASs, using data from six common human diseases with sufficient GWAS information. We show that although PRS accuracy has grown rapidly over the years, the pace of improvement from recent GWAS has decreased substantially, suggesting that merely increasing GWAS sample sizes may lead to only modest improvements in risk discrimination. We next investigated the factors influencing the maximum achievable prediction using whole-genome sequencing data from 125,000 UK Biobank participants and state-of-the-art modeling of polygenic outcomes. Our analyses suggest that increasing the variant coverage of PRS, using either more imputed variants or sequencing data, is a key component for future improvements in prediction accuracy.

AB - Polygenic risk scores (PRSs) models trained from genome-wide association study (GWAS) results are set to play a pivotal role in biomedical research addressing multifactorial human diseases. The prospect of using these risk scores in clinical care and public health is generating both enthusiasm and controversy, with varying opinions among experts about their strengths and limitations. The performance of existing polygenic scores is still limited but is expected to improve with increasing GWAS sample sizes and the development of new, more powerful methods. Theoretically, the variance explained by PRS can be as high as the total additive genetic variance, but it is unclear how much of that variance has already been captured by PRS. Here, we conducted a retrospective analysis to assess progress in PRS prediction accuracy since the publication of the first large-scale GWASs, using data from six common human diseases with sufficient GWAS information. We show that although PRS accuracy has grown rapidly over the years, the pace of improvement from recent GWAS has decreased substantially, suggesting that merely increasing GWAS sample sizes may lead to only modest improvements in risk discrimination. We next investigated the factors influencing the maximum achievable prediction using whole-genome sequencing data from 125,000 UK Biobank participants and state-of-the-art modeling of polygenic outcomes. Our analyses suggest that increasing the variant coverage of PRS, using either more imputed variants or sequencing data, is a key component for future improvements in prediction accuracy.

KW - GWAS

KW - polygenic risk prediction

KW - polygenicity

KW - sample size

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VL - 6

JO - Human Genetics and Genomics Advances

JF - Human Genetics and Genomics Advances

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M1 - 100457

ER -

Polygenic risk score prediction accuracy convergence

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Keywords

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