title: Multiplex Diagnosis of Oncogenic Fusion and MET Exon Skipping by Molecular Counting Using Formalin-Fixed Paraffin Embedded Lung Adenocarcinoma Tissues.
abstract: BACKGROUND
  Fusions of the anaplastic lymphoma receptor tyrosine kinase gene (ALK), ret proto-oncogene (RET), ROS proto-oncogene 1, receptor tyrosine kinase gene (ROS1), B-Raf proto-oncogene, serine/threonine kinase gene (BRAF), and neuregulin 1 gene (NRG1) and intronic MMNG HOS Transforming gene (MET) mutations are druggable oncogene alterations in lung adenocarcinoma that cause expression of aberrant transcripts. Because these aberrant transcripts are both infrequent (incidence <5%) and mutually exclusive, multiplex assays are required to detect them in tumor samples.
  
  
  METHODS
  Aberrant transcripts of the six aforementioned oncogenes (36 transcripts in total) were examined in a molecular counting (MC) assay, which counts RNA molecules by simultaneous hybridization of several probes. Forty-one samples of surgically resected lung adenocarcinoma tissue found to express one of these aberrant oncogenic transcripts upon whole transcriptome sequencing (test cohort: n = 22) or reverse transcription polymerase chain reaction (validation cohort: n = 19) analyses were subjected to MC, after which biopsies were performed on tumor tissue samples.
  
  
  RESULTS
  Threshold values for the diagnosis of each of the 36 transcripts were determined in frozen and formalin-fixed paraffin-embedded samples from the test cohort. On the basis of these threshold values, the MC assay diagnosed expression of oncogenic transcripts in the validation cohort samples with 100% accuracy. The assay also accurately detected oncogenic fusions in bronchial lavage fluid and transbronchial biopsy samples.
  
  
  CONCLUSIONS
  The MC assay allows multiplex detection of oncogenic fusion and exon-skipped transcripts in tumor samples, including in formalin-fixed paraffin-embedded samples obtained in the clinic.
authors: Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan; Course of Advanced Clinical Research of Cancer, Juntendo University Graduate School of Medicine, Tokyo, Japan.
authors: Kuniko
authors: K
authors: Sunami
authors: Division of Clinical Laboratory, National Cancer Center Hospital, Tokyo, Japan.
authors: Koh
authors: K
authors: Furuta
authors: Division of Pathology, National Cancer Center Research Institute, Tokyo, Japan.
authors: Koji
authors: K
authors: Tsuta
authors: Department of Endoscopy, Respiratory Endoscopy Division, National Cancer Center Research Institute, Tokyo, Japan.
authors: Shinji
authors: S
authors: Sasada
authors: Department of Endoscopy, Respiratory Endoscopy Division, National Cancer Center Research Institute, Tokyo, Japan.
authors: Takehiro
authors: T
authors: Izumo
authors: Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan.
authors: Takashi
authors: T
authors: Nakaoku
authors: Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan.
authors: Yoko
authors: Y
authors: Shimada
authors: Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan.
authors: Motonobu
authors: M
authors: Saito
authors: Department of Thoracic Oncology, National Cancer Center Research Institute, Tokyo, Japan.
authors: Hiroshi
authors: H
authors: Nokihara
authors: Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan.
authors: Shun-Ichi
authors: S
authors: Watanabe
authors: Department of Thoracic Oncology, National Cancer Center Research Institute, Tokyo, Japan; Course of Advanced Clinical Research of Cancer, Juntendo University Graduate School of Medicine, Tokyo, Japan.
authors: Yuichiro
authors: Y
authors: Ohe
authors: Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan. Electronic address: tkkohno@ncc.go.jp.
authors: Takashi
authors: T
authors: Kohno
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics*; D000077192:Adenocarcinoma of Lung; D005091:Exons; D005557:Formaldehyde; D050939:Gene Fusion; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D016612:Paraffin Embedding; D000090063:Proto-Oncogene Mas; D019859:Proto-Oncogene Proteins c-met / Q000235:genetics*; D012333:RNA, Messenger / Q000032:analysis
chemical_list: C000715470:MAS1 protein, human; D000090063:Proto-Oncogene Mas; D012333:RNA, Messenger; D005557:Formaldehyde; C491743:MET protein, human; D019859:Proto-Oncogene Proteins c-met
keywords: Genetic diagnosis; MET exon skipping; Molecular counting; Oncogene fusion; Personalized medicine