title: Comparison of Direct Sequencing, PNA Clamping-Real Time Polymerase Chain Reaction, and Pyrosequencing Methods for the Detection of EGFR Mutations in Non-small Cell Lung Carcinoma and the Correlation with Clinical Responses to EGFR Tyrosine Kinase Inhibitor Treatment.
abstract: BACKGROUND
  The aims of this study were to evaluate the abilities of direct sequencing (DS), peptide nucleic acid (PNA) clamping, and pyrosequencing methods to detect epidermal growth factor receptor (EGFR) mutations in formalin-fixed paraffin-embedded (FFPE) non-small cell lung carcinoma (NSCLC) samples and to correlate EGFR mutational status as determined by each method with the clinical response to EGFR tyrosine kinase inhibitors (TKIs).
  
  
  METHODS
  Sixty-one NSCLC patients treated with EGFR TKIs were identified to investigate somatic mutations in the EGFR gene (exons 18-21).
  
  
  RESULTS
  Mutations in the EGFR gene were detected in 38 of the 61 patients (62%) by DS, 35 (57%) by PNA clamping and 37 (61%) by pyrosequencing. A total of 44 mutations (72%) were found by at least one of the three methods, and the concordances among the results were relatively high (82-85%; kappa coefficient, 0.713 to 0.736). There were 15 discordant cases (25%) among the three different methods.
  
  
  CONCLUSIONS
  All three EGFR mutation tests had good concordance rates (over 82%) for FFPE samples. These results suggest that if the DNA quality and enrichment of tumor cells are assured, then DS, PNA clamping, and pyrosequencing are appropriate methods for the detection of EGFR mutations.
authors.affiliation: Department of Pathology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea. ; Department of Pathology, Soonchunhyang University Cheonan Hospital, Soonchunhyang University College of Medicine, Cheonan, Korea.
authors.forename: Hyun Ju
authors.initials: HJ
authors.lastname: Lee
authors.forename: Xianhua
authors.initials: X
authors.lastname: Xu
authors.forename: Hyojin
authors.initials: H
authors.lastname: Kim
authors.forename: Yan
authors.initials: Y
authors.lastname: Jin
authors.forename: Pingli
authors.initials: P
authors.lastname: Sun
authors.forename: Ji Eun
authors.initials: JE
authors.lastname: Kim
authors.forename: Jin-Haeng
authors.initials: JH
authors.lastname: Chung
keywords: Lung neoplasms; Mutation; Peptide nucleic acids; Pyrosequencing; Receptor, epidermal growth factor; Sequencing analysis, DNA