Artificial Intelligence and Multi-Omics in Pharmacogenomics: A New Era of Precision Medicine

Pharmacogenomics is entering a transformative phase as high-throughput “omics” techniques become increasingly integrated with state-of-the-art artificial intelligence (AI) methods. Although early successes in single-gene pharmacogenetics reported clear clinical benefits, many drug response phenotypes are governed by intricate networks of genomic variants, epigenetic modifications, and metabolic pathways. Multi-omics approaches address this complexity by capturing genomic, transcriptomic, proteomic, and metabolomic data layers, offering a comprehensive view of patient-specific biology. Advanced AI models, including deep neural networks, graph neural networks, and representation learning techniques, further enhance this landscape by detecting hidden patterns, filling gaps in incomplete data sets, and enabling in silico simulations of treatment responses. Such capabilities not only improve predictive accuracy but also deepen mechanistic insights, revealing how gene–gene and gene–environment interactions shape therapeutic outcomes. At the same time, real-world data from diverse patient populations is broadening the evidence base, underscoring the importance of inclusive datasets and population-specific algorithms to reduce health disparities. Despite challenges related to data harmonization, interpretability, and regulatory oversight, the synergy between multi-omics integration and AI-driven analytics holds relevant promise for revolutionizing clinical decision-making. In this review, we highlighted key technological advances, discussed current limitations, and outlined future directions for translating multi-omics plus AI innovations into routine personalized medicine.