title: Epidermal Growth Factor Receptor Mutation and Anaplastic Lymphoma Kinase Gene Fusion: Detection in Malignant Pleural Effusion by RNA or PNA Analysis.
abstract: Analyzing EGFR mutations and detecting ALK gene fusion are indispensable when planning to treat pulmonary adenocarcinoma. Malignant pleural effusion (MPE) is a devastating complication of lung cancer and sometimes the only source for mutation analysis. The percentage of tumor cells in the pleural effusion may be low; therefore, mutant enrichment is required for a successful analysis. The EGFR mutation status in MPE was determined using three methods: (1) PCR sequencing of genomic DNA (direct sequencing), (2) mutant-enriched PCR sequencing of genomic DNA using peptide nucleic acid (PNA-sequencing), and (3) PCR sequencing of cDNA after reverse transcription for cellular RNA (RNA-sequencing). RT-PCR was also used to test cases for ALK gene fusion. PNA-sequencing and RNA-sequencing had similar analytical sensitivities (< 1%), which indicates similar enrichment capabilities. The clinical sensitivity in 133 cases when detecting the common EGFR exon 19 and exon 21 mutations was 56.4% (75/133) for direct sequencing, 63.2% (84/133) for PNA-sequencing, and 65.4% (87/133) for RNA-sequencing. RT-PCR and sequencing showed 5 cases (3.8%) with ALK gene fusion. All had wild-type EGFR. For EGFR analysis of MPE, RNA-sequencing is at least as sensitive as PNA-sequencing but not limited to specific mutations. Detecting ALK fusion can be incorporated in the same RNA workflow. Therefore, RNA is a better source for comprehensive molecular diagnoses in MPE.
authors.affiliation: Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan.|Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University Hospital, Tainan, Taiwan.|College of Medicine, Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.|The Association of Medical Technologists, Tainan, Taiwan.
authors.forename: Yi-Lin
authors.initials: YL
authors.lastname: Chen
authors.affiliation: Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan.|College of Medicine, Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.|The Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.
authors.forename: Chung-Ta
authors.initials: CT
authors.lastname: Lee
authors.affiliation: Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan.|College of Medicine, Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.|The Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.|The Institute of Molecular Medical, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.|The Association of Medical Technologists, Tainan, Taiwan.
authors.forename: Cheng-Chan
authors.initials: CC
authors.lastname: Lu
authors.affiliation: Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan.|College of Medicine, Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.|The Association of Medical Technologists, Tainan, Taiwan.
authors.forename: Shu-Ching
authors.initials: SC
authors.lastname: Yang
authors.affiliation: Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan.|College of Medicine, Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.|The Association of Medical Technologists, Tainan, Taiwan.
authors.forename: Wan-Li
authors.initials: WL
authors.lastname: Chen
authors.affiliation: Division of Hematology/Oncology, Department of Internal Medicine, Tainan Municipal Hospital, Tainan, Taiwan.
authors.forename: Yang-Cheng
authors.initials: YC
authors.lastname: Lee
authors.affiliation: Yuan's General Hospital, Kaohsiung, Taiwan.
authors.forename: Chung-Hsien
authors.initials: CH
authors.lastname: Yang
authors.affiliation: Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan.
authors.forename: Shu-Ling
authors.initials: SL
authors.lastname: Peng
authors.affiliation: Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan.|College of Medicine, Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.|The Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.|The Institute of Molecular Medical, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.
authors.forename: Wu-Chou
authors.initials: WC
authors.lastname: Su
authors.affiliation: Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan.|College of Medicine, Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.|The Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.|The Institute of Molecular Medical, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.
authors.forename: Nan-Haw
authors.initials: NH
authors.lastname: Chow
authors.affiliation: Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan.|Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University Hospital, Tainan, Taiwan.|College of Medicine, Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.|The Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.|The Institute of Molecular Medical, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.
authors.forename: Chung-Liang
authors.initials: CL
authors.lastname: Ho
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000077548:Anaplastic Lymphoma Kinase; D014408:Biomarkers, Tumor / Q000235:genetics / Q000592:standards*; D016022:Case-Control Studies; D045744:Cell Line, Tumor; D066246:ErbB Receptors / Q000235:genetics*; D005260:Female; D050939:Gene Fusion; D006801:Humans; D008297:Male; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques / Q000592:standards; D009154:Mutation; D016066:Pleural Effusion, Malignant / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D020794:Receptor Protein-Tyrosine Kinases / Q000235:genetics*; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA / Q000592:standards
chemical_list: D014408:Biomarkers, Tumor; C000626173:ALK protein, human; D000077548:Anaplastic Lymphoma Kinase; C512478:EGFR protein, human; D066246:ErbB Receptors; D020794:Receptor Protein-Tyrosine Kinases