A network model for patient-derived drug response in breast cancer integrating multi-omics datasets. (PubMed, bioRxiv)
PDDRNet-MH achieved consistently high accuracy, with perfect prediction scores for gemcitabine and vinorelbine (Area Under the Receiver Operating Characteristic Curve [AUC-ROC] = 1.00; Area Under the Precision-Recall Curve [AUC-PR] = 1.00) and near-perfect scores for methotrexate and zoledronate (AUC-ROC = 0.95; AUC-PR = 0.99), demonstrating its ability to robustly distinguish sensitive from resistant patients. Biologically, PDDRNet-MH accurately prioritized established clinical biomarkers, including HER2 (ERBB2) for lapatinib and BRCA1/2 for doxorubicin and cyclophosphamide. Beyond known associations, the model identified additional genes within the HER2 amplicon on chromosome 17q12, including STARD3, MIEN1, and PPP1R1B, whose amplification was significantly associated with elevated drug response scores, suggesting potential roles in HER2-targeted therapy. These findings highlight the ability of PDDRNet-MH to recover and extend clinically relevant drug-biomarker associations, supporting its utility in guiding precision oncology.