XPRS: a tool for interpretable and explainable polygenic risk score.

Abstract

Summary: The polygenic risk score (PRS) is an important method for assessing genetic susceptibility to diseases; however, its clinical utility is limited by a lack of interpretability tools. To address this problem, we introduce eXplainable PRS (XPRS), an interpretation and visualization tool that decomposes PRSs into genes/regions and single nucleotide polymorphism (SNP) contribution scores via Shapley additive explanations (SHAPs), which provide insights into specific genes and SNPs that significantly contribute to the PRS of an individual. This software features a multilevel visualization approach, including Manhattan plots, LocusZoom-like plots, and tables at the population and individual levels, to highlight important genes and SNPs. By implementing with a user-friendly web interface, XPRS allows for straightforward data input and interpretation. By bridging the gap between complex genetic data and actionable clinical insights, XPRS can improve communication between clinicians and patients.

Availability and implementation: The XPRS software is publicly available on GitHub at https://github.com/nayeonkim93/XPRS and can see the demo through our cloud-based web service at https://xprs.leelabsg.org/.