title: Comparison of next generation sequencing, SNaPshot assay and real-time polymerase chain reaction for lung adenocarcinoma EGFR mutation assessment.
abstract: BACKGROUND
  The epidermal growth factor receptor (EGFR) mutation status assessment has become increasingly important given the significant impact of tyrosine kinase inhibitors in lung cancer management. Our aim was to compare real life operational characteristics for three EGFR mutation assays - two targeted approaches and a next generation sequencing (NGS) technique.
  
  
  METHODS
  EGFR mutation status was assessed for lung adenocarcinoma samples (formalin fixed- paraffin embedded samples) using qPCR, SNaPshot and NGS (Ion Torrent™) techniques.
  
  
  RESULTS
  A total of 15 high clinical significance mutations were identified by at least one technique from the total of 64 samples. All mutations were identified by the TaqMan qPCR technique while SNaPshot in conjunction with fragment analysis identified 11 EGFR mutations. The NGS approach followed by an automatic analysis using the default calling parameters identified 10 mutations from the SNaPshot/qPCR panel and other three insertions, five point mutations and 58 silent variants; manual data review identified all 15 high significance mutations.
  
  
  CONCLUSIONS
  Performance was similar for high tumor content samples but careful data analysis and post hoc variant calling filter alterations were necessary in order to obtain robust results from low tumor content samples by NGS. NGS is able to generate a comprehensive mutational profile albeit at a higher cost and workload. Result interpretation should take into account not only general run parameters such as mean read depth but also relative coverage and read distribution; currently there is an acute need to define firm recommendations/standards concerning NGS data interpretation and quality control.
authors.affiliation: Department of Thoracic Oncology, Regional Institute of Oncology, University of Medicine and Pharmacy Iasi, Str. Gen. Berthelot, 2-4, Iasi, 700384, Romania.
authors.forename: Andrei-Tudor
authors.initials: AT
authors.lastname: Cernomaz
authors.affiliation: Lung Cancer Molecular Diagnostic Laboratory, University of Medicine and Pharmacy Iasi, Iasi, Romania.
authors.forename: Ina Iuliana
authors.initials: II
authors.lastname: Macovei
authors.affiliation: Lung Cancer Molecular Diagnostic Laboratory, University of Medicine and Pharmacy Iasi, Iasi, Romania.
authors.forename: Ionut
authors.initials: I
authors.lastname: Pavel
authors.affiliation: Pathology Department, University of Medicine and Pharmacy Iasi, Iasi, Romania.
authors.forename: Carmen
authors.initials: C
authors.lastname: Grigoriu
authors.affiliation: Oncology Department, Regional Institute of Oncology, University of Medicine and Pharmacy Iasi, Iasi, Romania.
authors.forename: Mihai
authors.initials: M
authors.lastname: Marinca
authors.affiliation: Department of Pulmonary Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland.
authors.forename: Florent
authors.initials: F
authors.lastname: Baty
authors.affiliation: Lung Cancer Molecular Diagnostic Laboratory, University of Medicine and Pharmacy Iasi, Iasi, Romania.
authors.forename: Simona
authors.initials: S
authors.lastname: Peter
authors.affiliation: Lung Cancer Molecular Diagnostic Laboratory, University of Medicine and Pharmacy Iasi, Iasi, Romania.
authors.forename: Radu
authors.initials: R
authors.lastname: Zonda
authors.affiliation: Department of Pulmonary Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland.
authors.forename: Martin
authors.initials: M
authors.lastname: Brutsche
authors.affiliation: Department of Thoracic Oncology, Regional Institute of Oncology, University of Medicine and Pharmacy Iasi, Str. Gen. Berthelot, 2-4, Iasi, 700384, Romania. b_grigoriu@hotmail.com.|Lung Cancer Molecular Diagnostic Laboratory, University of Medicine and Pharmacy Iasi, Iasi, Romania. b_grigoriu@hotmail.com.
authors.forename: Bogdan- Dragos
authors.initials: B
authors.lastname: Grigoriu
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics*; D000077192:Adenocarcinoma of Lung; D000368:Aged; D004252:DNA Mutational Analysis / Q000379:methods*; D066246:ErbB Receptors / Q000235:genetics*; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D009154:Mutation; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*
chemical_list: C512478:EGFR protein, human; D066246:ErbB Receptors