The application of clinical pharmacogenetics in precision medicine: identification of germline and somatic mutations as biomarkers of drug response in solid tumors

Precision medicine has transformed contemporary oncology. It integrates molecular, genetic, and clinical data to guide therapeutic decisions. Combining pharmacogenetics for germline variants assessment with liquid biopsy analysis of cell-free DNA (cfDNA) offers valuable insights into tumor evolution under therapy. This approach improves patient stratification, treatment optimization, and clinical outcomes. This PhD thesis comprises four sections. It adopts an integrated approach, combining pharmacogenetic profiling, circulating tumor DNA (ctDNA)-based liquid biopsy, and longitudinal disease monitoring across multiple solid tumors. Germline variants were analyzed using Real-Time PCR from whole blood. Somatic alterations were assessed in plasma-derived cfDNA using digital PCR and Next-Generation Sequencing. Section I reports a second-line clinical trial in advanced pancreatic ductal adenocarcinoma comparing nal-IRI plus S-1 versus nal-IRI plus 5-fluorouracil/leucovorin. Integrated germline (DPYD, UGT1A1) and somatic (KRAS) analyses supported the superior safety and efficacy of nal-IRI plus 5-fluorouracil/leucovorin and demonstrated the prognostic value of ctDNA-based KRAS monitoring. Section II evaluates clinical determinants of ctDNA shedding in EGFR-mutant Non-Small Cell Lung cancer, highlighting the importance of integrating clinical features to correctly interpret liquid biopsy results and avoid false-negative findings. Section III demonstrates the feasibility and prognostic relevance of detecting the IDH1 R132H mutation in plasma cfDNA from glioma patients, despite the presence of the blood–brain barrier. Section IV assesses the clinical impact of DPYD variants in patients receiving fluoropyrimidines, demonstrating limited predictive value of the c.1236G>A/HapB3 variant for severe toxicity and supporting individualized dosing strategies. Overall, this work underscores the clinical value of integrating pharmacogenetics, ctDNA analysis, and clinical data to advance precision oncology and optimize cancer treatment in real-world settings.