title: Detection of MET Gene Copy Number in Cancer Samples Using the Droplet Digital PCR Method.
abstract: OBJECTIVE
  The 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.
  
  
  METHODS
  The 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.
  
  
  RESULTS
  In 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).
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: Amgen Biopharmaceutical Research & Development (Shanghai) Co., Ltd, Shanghai, China.
authors.forename: Yanni
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Amgen Biopharmaceutical Research & Development (Shanghai) Co., Ltd, Shanghai, China.
authors.forename: En-Tzu
authors.initials: ET
authors.lastname: Tang
authors.affiliation: Amgen Biopharmaceutical Research & Development (Shanghai) Co., Ltd, Shanghai, China.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Du
mesh_terms: D014408:Biomarkers, Tumor; D045744:Cell Line, Tumor; D056915:DNA Copy Number Variations; D005784:Gene Amplification; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D009369:Neoplasms / Q000188:drug therapy / Q000235:genetics* / Q000473:pathology; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D019859:Proto-Oncogene Proteins c-met / Q000235:genetics*
chemical_list: D014408:Biomarkers, Tumor; C491743:MET protein, human; D019859:Proto-Oncogene Proteins c-met