ArticleNature communications2024
Tuning parameters for polygenic risk score methods using GWAS summary statistics from training data.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- MIXPRS enables multi-population and multi-method polygenic risk scores using summary statistics.Nature genetics · 2026Article
- Divergent autoimmune genetic landscapes in diabetic and non-diabetic individuals.BMC genomic data · 2026Article
- Integrating common and rare variants improves polygenic risk prediction across diverse populations.Nature communications · 2026Article
- PreoperativeFrontiers in bioinformatics · 2026Review
- Improving performance of polygenic risk scores for hypertension across two ancestry groups.PloS one · 2026Article
- Improving performance of polygenic risk scores for hypertension across two ancestry groups.medRxiv : the preprint server for health sciences · 2025Article
- GRPa-PRS: A risk stratification method to identify genetically-regulated pathways in polygenic diseases.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- Data sharing in the PRIMED Consortium: Design, implementation, and recommendations for future policymaking.American journal of human genetics · 2025Review
- Almost Free Enhancement of Multi-Population PRS: From Data-Fission to Pseudo-GWAS Subsampling.bioRxiv : the preprint server for biology · 2025Article
- Genome-wide association studies, Polygenic Risk Scores and Mendelian randomisation: an overview of common genetic epidemiology methods for ophthalmic clinicians.The British journal of ophthalmology · 2025Review
- Polygenic risk and rare variant gene clustering enhance cancer risk stratification for breast and prostate cancers.Communications biology · 2024Article
- Fast and scalable ensemble learning method for versatile polygenic risk prediction.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Tuning parameters for polygenic risk score methods using GWAS summary statistics from training data.Nature communications · 2024Article
- Risk of adverse cardiovascular events based on common genetic variants in 8-year follow-up of the LIPIDOGEN2015 population using the polygenic risk score (PRS): study design and methodology.Archives of medical science : AMS · 2024Article
- Leveraging genetic correlations and multiple populations to improve genetic risk prediction for non-European populations.Research square · 2023Article
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Abstract
Various polygenic risk scores (PRS) methods have been proposed to combine the estimated effects of single nucleotide polymorphisms (SNPs) to predict genetic risks for common diseases, using data collected from genome-wide association studies (GWAS). Some methods require external individual-level GWAS dataset for parameter tuning, posing privacy and security-related concerns. Leaving out partial data for parameter tuning can also reduce model prediction accuracy. In this article, we propose PRStuning, a method that tunes parameters for different PRS methods using GWAS summary statistics from the training data. PRStuning predicts the PRS performance with different parameters, and then selects the best-performing parameters. Because directly using training data effects tends to overestimate the performance in the testing data, we adopt an empirical Bayes approach to shrinking the predicted performance in accordance with the genetic architecture of the disease. Extensive simulations and real data applications demonstrate PRStuning's accuracy across PRS methods and parameters.
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