Machine learning models for pharmacogenomic variant effect predictions - recent developments and future frontiers

Pharmacogenomic variations in genes involved in drug disposition and in drug targets is a major determinant of inter-individual differences in drug response and toxicity. While the effects of common variants are well established, millions of rare variations remain functionally uncharacterized, posing a challenge for the implementation of precision medicine. Recent advances in machine learning (ML) have significantly enhanced the prediction of variant effects by considering DNA as well as protein sequences, as well as their evolutionary conservation and haplotype structures. Emerging deep learning models utilize techniques to capture evolutionary conservation and biophysical properties, and ensemble approaches that integrate multiple predictive models exhibit increased accuracy, robustness, and interpretability. This review explores the current landscape of ML-based variant effect predictors. We discuss key methodological differences and highlight their strengths and limitations for pharmacogenomic applications. We furthermore discuss emerging methodologies for the prediction of substrate-specificity and for consideration of variant epistasis. Combined, these tools improve the functional effect prediction of drug-related variants and offer a viable strategy that could in the foreseeable future translate comprehensive genomic information into pharmacogenetic recommendations.