ArticleGenome medicine2025
STREAM-PRS: a multi-tool pipeline for streamlining polygenic risk score computation.
Article in Genome medicine, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Evidence standards for multi-ancestry polygenic prediction.Genome biology · 2026Review
- STREAM-PRS: a multi-tool pipeline for streamlining polygenic risk score computation.Genome medicine · 2025Article
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Authors and funding
6 authors.
Funding
Abstract
backgroundPolygenic risk scores (PRS) offer an elegant approach to estimating an individual's genetic predisposition to a given disease or trait. Numerous tools are available for PRS calculation, each applying different strategies to account for linkage disequilibrium and effect size shrinkage. No single tool is inherently superior. Therefore, multiple tools should be tested to identify the one that best suits the research question. Additionally, challenges such as population stratification and PRS portability further complicate the field. Here, we developed STREAM-PRS, a PRS pipeline designed to calculate scores using five popular tools: PRSice-2, PRS-CS, LDpred2, lassosum, and lassosum2.
methodsSTREAM-PRS first computes scores under various settings in a training dataset. The selected variants are subsequently used for score calculation in the test dataset, followed by PC correction and standardization to improve portability across different centers. Finally, the pipeline determines the best PRS tool and settings based on the variance explained (R
resultsUsing STREAM-PRS for 472 scores across the 5 PRS tools with 404 individuals in the training and 1000 individuals in the test dataset takes approximately 20 h to complete. For IBD, lassosum was identified as the best-performing tool with optimal settings as follows: a shrinkage value of 0.7 and a lambda value of 0.008859. Applying this optimized PRS to our in-house IBD dataset (validation) resulted in an R
conclusionsOverall, STREAM-PRS provides an efficient framework for selecting the best PRS calculation strategy and helps bridge the portability gap within the PRS field. STREAM-PRS is available at https://github.com/SaraBecelaere/STREAM-PRS.
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Registered trials
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