Bioinformatic challenges for pharmacogenomic study: tools for genomic data analysis

The sequencing of the human genome in 2003 marked a transformative shift from a one-size-fits-all approach to personalized medicine, emphasizing patient-specific molecular and physiological characteristics. Advances in sequencing technologies, from Sanger methods to Next-Generation Sequencing (NGS), have generated vast genomic datasets, enabling the development of tailored therapeutic strategies. Pharmacogenomics (PGx) has played a pivotal role in elucidating how the genetic make-up influences inter-individual variability in drug efficacy and toxicity discovering predictive and prognostic biomarkers. However, challenges persist in interpreting polymorphic variants and translating findings into clinical practice. Multi-omics data integration and bioinformatics tools are essential for addressing these complexities, uncovering novel molecular insights, and advancing precision medicine. In this review, starting from our experience in PGx studies performed by DMET microarray platform, we propose a guideline combining machine learning, statistical, and network-based approaches to simplify and better understand complex DMET PGx data analysis which can be adapted for broader PGx applications, fostering accessibility to high-performance bioinformatics, also for non-specialists. Moreover, we describe an example of how bioinformatic tools can be used for a comprehensive integrative analysis which could allow the translation of genetic insights into personalized therapeutic strategies.