Kuniko Sunami1, Koh Furuta2, Koji Tsuta3, Shinji Sasada4, Takehiro Izumo4, Takashi Nakaoku5, Yoko Shimada5, Motonobu Saito5, Hiroshi Nokihara6, Shun-Ichi Watanabe7, Yuichiro Ohe8, Takashi Kohno9. 1. 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. 2. Division of Clinical Laboratory, National Cancer Center Hospital, Tokyo, Japan. 3. Division of Pathology, National Cancer Center Research Institute, Tokyo, Japan. 4. Department of Endoscopy, Respiratory Endoscopy Division, National Cancer Center Research Institute, Tokyo, Japan. 5. Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan. 6. Department of Thoracic Oncology, National Cancer Center Research Institute, Tokyo, Japan. 7. Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan. 8. 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. 9. Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan. Electronic address: tkkohno@ncc.go.jp.
Abstract
INTRODUCTION: 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.
INTRODUCTION: 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: Johanna S M Mattsson; Hans Brunnström; Verena Jabs; Karolina Edlund; Karin Jirström; Stephanie Mindus; Linnéa la Fleur; Fredrik Pontén; Mats G Karlsson; Christina Karlsson; Hirsh Koyi; Eva Brandén; Johan Botling; Gisela Helenius; Patrick Micke; Maria A Svensson Journal: BMC Cancer Date: 2016-08-05 Impact factor: 4.430
Authors: Kajsa Ericson Lindquist; Anna Karlsson; Per Levéen; Hans Brunnström; Christel Reuterswärd; Karolina Holm; Mats Jönsson; Karin Annersten; Frida Rosengren; Karin Jirström; Jaroslaw Kosieradzki; Lars Ek; Åke Borg; Maria Planck; Göran Jönsson; Johan Staaf Journal: Oncotarget Date: 2017-05-23
Authors: Anna Karlsson; Helena Cirenajwis; Kajsa Ericson-Lindquist; Hans Brunnström; Christel Reuterswärd; Mats Jönsson; Cristian Ortiz-Villalón; Aziz Hussein; Bengt Bergman; Anders Vikström; Nastaran Monsef; Eva Branden; Hirsh Koyi; Luigi de Petris; Patrick Micke; Annika Patthey; Annelie F Behndig; Mikael Johansson; Maria Planck; Johan Staaf Journal: Sci Rep Date: 2019-03-26 Impact factor: 4.379