Detection of MET Gene Copy Number in Cancer Samples Using the Droplet Digital PCR Method

Abstract

PurposeThe analysis of MET gene copy number (CN) has been considered to be a potential biomarker to predict the response to MET-targeted therapies in various cancers. However, the current standard methods to determine MET CN are SNP 6.0 in the genomic DNA of cancer cell lines and fluorescence in situ hybridization (FISH) in tumor models, respectively, which are costly and require advanced technical skills and result in relatively subjective judgments. Therefore, we employed a novel method, droplet digital PCR (ddPCR), to determine the MET gene copy number with high accuracy and precision.MethodsThe genomic DNA of cancer cell lines or tumor models were tested and compared with the MET gene CN and MET/CEN-7 ratio determined by SNP 6.0 and FISH, respectively.ResultsIn cell lines, the linear association of the MET CN detected by ddPCR and SNP 6.0 is strong (Pearson correlation = 0.867). In tumor models, the MET CN detected by ddPCR was significantly different between the MET gene amplification and non-amplification groups according to FISH (mean: 15.4 vs 2.1; P = 0.044). Given that MET gene amplification is defined as MET CN >5.5 by ddPCR, the concordance rate between ddPCR and FISH was 98.0%, and Cohen's kappa coefficient was 0.760 (95% CI, 0.498–1.000; P <0.001).ConclusionsThe results demonstrated that the ddPCR method has the potential to quantify the MET gene copy number with high precision and accuracy as compared with the results from SNP 6.0 and FISH in cancer cell lines and tumor samples, respectively.

Original Article. Prevalence of HPV16 IgG Antibody and Rt-Pcr DNAdetection in Patients with Laryngeal Carcinoma and Cervical Dysplasia

“…Diagnosis of infection caused by oncogenic types of HPVs is of great importance for prevention, early detection and proper treatment of affected patients. In this sense, the methods applied in this study (RT-PCR and ELISA) are current, specific, credible and consistent with research in other countries [5].…”

Detection of MET Alterations Using Cell Free DNA and Circulating Tumor Cells from Cancer Patients

“…In addition to the CTCs analysis, we demonstrated the ddPCR approach to be a useful tool for detecting MET amplification in plasma samples from cancer patients. Zhang et al had already shown this capacity, detecting MET CN in genomic DNA from cancer cell lines and tumor samples [24]. Recently, a study in cfDNA obtained from plasma of different tumor types showed that detection of MET alterations (amplification and point mutations) by liquid biopsy was feasible using the Guardant360 NGS panel [25].…”

A first-in-human phase I study of SAR125844, a selective MET tyrosine kinase inhibitor, in patients with advanced solid tumours with MET amplification

“…amplification [25]). These criteria may have led to a low percentage of patients with very high MET-amplified tumours, potentially leading to suboptimal enrichment of the most responsive patients.…”