Extrachromosomal DNA (ecDNA) has appeared as a key driver of oncogene amplification, tumor heterogeneity, and therapeutic resistance, thereby reshaping the paradigm of precision oncology―particularly in metastatic and treatment-refractory cancers. However, the clinical translation of ecDNA-based discoveries into scalable therapeutic applications remains limited. This study introduces an integrated, empirically validated precision oncology platform that combines ecDNA biomarker profiling, artificial intelligence (AI)-driven multiomics modeling, and clustered regularly interspaced short palindromic repeats (CRISPR)-based functional validation. Built upon the “9 Building Blocks” business model, the platform incorporates high-resolution ecDNA detection (via whole-genome sequencing, fluorescence in situ hybridization, and Amplicon Architect), single-cell and spatial transcriptomics, and machine learning-based therapeutic response prediction. The AI-integrated multi-omics framework achieved robust predictive accuracy (area under the curve > .90) across diverse tumor types and was functionally validated through patient-derived xenograft models and CRISPR-Cas9 gene screening. Specifically, CRISPR knockdown experiments that target ecDNA-associated oncogenes (e.g., Myelocytomatosis oncogene, epidermal growth factor receptor) demonstrated high knockdown efficiency (up to 82% using quantitative polymerase chain reaction), significantly reduced cell viability (up to 45%), increased apoptosis (up to 38%), and suppressed tumor growth in vivo (up to 53% reduction in volume, p < .001), confirming their biological and therapeutic relevance. A pilot study that involved 12 patients further demonstrated concordance between liquid biopsy-derived ecDNA profiles and tissue biopsy results, whereas a structured stakeholder survey (n = 47) yielded strong consensus on the platform’s clinical relevance (4.62/5), feasibility (4.45/5), and strategic value (4.58/5). These results underscore the platform’s technical robustness, translational potential, and commercialization readiness for ecDNA-guided precision therapeutics.
