Multiplex Droplet Digital PCR Assay for Detection of MET and HER2 Genes Amplification in Non-Small Cell Lung Cancer

SIMPLE SUMMARY: Non-small-cell lung cancer (NSCLC) remains one of the most common tumors with a high mortality and morbidity rate. Alterations in HER2 and MET could be a target for anti-tumor drugs or lead to resistance to anti-EGFR therapeutics. Existing methods for detecting HER2 and MET amplifications are time and labor-consuming, and alternative methods are needed. We report the first multiplex droplet digital PCR (ddPCR) assay for the simultaneous detection of MET and HER2 amplification in NSCLC samples. The suitability of qPCR was assessed for the optimization of multiplex ddPCR, and optimal ddPCR conditions were selected. The developed ddPCR was validated on artificial samples with various DNA concentrations and MET and HER2 ratios. Using ddPCR, 436 EGFR-negative NSCLC samples were analyzed, and, among them, five specimens (1.15%) were MET-positive and six samples (1.38%) were HER2-positive. The multiplex ddPCR assay could be used for screening MET and HER2 amplification in NSCLC samples. ABSTRACT: Non-small-cell lung cancer (NSCLC), a subtype of lung cancer, remains one of the most common tumors with a high mortality and morbidity rate. Numerous targeted drugs were implemented or are now developed for the treatment of NSCLC. Two genes, HER2 and MET, are among targets for these specific therapeutic agents. Alterations in HER2 and MET could lead to primary or acquired resistance to commonly used anti-EGFR drugs. Using current methods for detecting HER2 and MET amplifications is time and labor-consuming; alternative methods are required for HER2 and MET testing. We developed the first multiplex droplet digital PCR assay for the simultaneous detection of MET and HER2 amplification in NSCLC samples. The suitability of qPCR was assessed for the optimization of multiplex ddPCR. The optimal elongation temperature, reference genes for DNA quantification, and amplicon length were selected. The developed ddPCR was validated on control samples with various DNA concentrations and ratios of MET and HER2 genes. Using ddPCR, 436 EGFR-negative NSCLC samples were analyzed. Among the tested samples, five specimens (1.15%) showed a higher ratio of MET, and six samples (1.38%) showed a higher ratio of HER2. The reported multiplex ddPCR assay could be used for the routine screening of MET and HER2 amplification in NSCLC samples.