A Novel Digital PCR Assay for Accurate Detection and Differentiation of Focal and Non-Focal Subtypes of Mesenchymal–Epithelial Transition (MET) Gene Amplification in Lung Cancer

Background/Objectives: Mesenchymal–epithelial transition (MET) gene amplification is a critical biomarker in non-small cell lung cancer (NSCLC), significantly influencing treatment decisions and prognostic evaluations. However, current detection methods such as fluorescence in situ hybridization (FISH) and next-generation sequencing (NGS) have limitations in speed, cost, and specificity, particularly when distinguishing between focal MET amplification and MET polysomy. Methods: This study introduces a novel digital PCR (dPCR) assay designed not only to detect MET amplification but also to differentiate between its focal and non-focal subtypes. The assay was evaluated against established FISH and targeted NGS panels using 55 NSCLC samples with known MET amplification statuses (26 positive and 29 negative) confirmed by FISH and NGS. Results The dPCR assay demonstrated high sensitivity (96.0%) and specificity (96.7%), achieving 100% concordance with FISH in differentiating focal MET amplification from MET polysomy. Additionally, the assay exhibited excellent precision, accuracy, and linearity (R2 = 1.00) in MET copy number quantification, surpassing NGS in diagnostic performance. Offering a robust, cost-effective, and efficient alternative to FISH, the dPCR assay significantly reduces the turnaround time (3 h versus 2 days) and provides a quantitative and objective method for MET amplification detection and subtype differentiation. This makes it suitable for clinical laboratories with limited molecular expertise. Conclusions: This study highlights the potential of the dPCR assay to complement existing molecular diagnostic techniques, delivering reliable and actionable results for MET-targeted therapy selection in NSCLC patients and thereby advancing precision oncology.