title: Targeted resequencing reveals ALK fusions in non-small cell lung carcinomas detected by FISH, immunohistochemistry, and real-time RT-PCR: a comparison of four methods.
abstract: Anaplastic lymphoma receptor tyrosine kinase (ALK) gene rearrangements occur in a subgroup of non-small cell lung carcinomas (NSCLCs). The identification of these rearrangements is important for guiding treatment decisions. The aim of our study was to screen ALK gene fusions in NSCLCs and to compare the results detected by targeted resequencing with results detected by commonly used methods, including fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and real-time reverse transcription-PCR (RT-PCR). Furthermore, we aimed to ascertain the potential of targeted resequencing in detection of ALK-rearranged lung carcinomas. We assessed ALK fusion status for 95 formalin-fixed paraffin-embedded tumor tissue specimens from 87 patients with NSCLC by FISH and real-time RT-PCR, for 57 specimens from 56 patients by targeted resequencing, and for 14 specimens from 14 patients by IHC. All methods were performed successfully on formalin-fixed paraffin-embedded tumor tissue material. We detected ALK fusion in 5.7% (5 out of 87) of patients examined. The results obtained from resequencing correlated significantly with those from FISH, real-time RT-PCR, and IHC. Targeted resequencing proved to be a promising method for ALK gene fusion detection in NSCLC. Means to reduce the material and turnaround time required for analysis are, however, needed.
authors.affiliation: Department of Pathology, Haartman Institute, University of Helsinki, P.O. Box 21 (Haartmaninkatu 3), 00014 Helsinki, Finland.
authors.forename: Katja
authors.initials: K
authors.lastname: Tuononen
authors.forename: Virinder Kaur
authors.initials: VK
authors.lastname: Sarhadi
authors.forename: Aino
authors.initials: A
authors.lastname: Wirtanen
authors.forename: Mikko
authors.initials: M
authors.lastname: Rönty
authors.forename: Kaisa
authors.initials: K
authors.lastname: Salmenkivi
authors.forename: Aija
authors.initials: A
authors.lastname: Knuuttila
authors.forename: Satu
authors.initials: S
authors.lastname: Remes
authors.forename: Aino I
authors.initials: AI
authors.lastname: Telaranta-Keerie
authors.forename: Stuart
authors.initials: S
authors.lastname: Bloor
authors.forename: Pekka
authors.initials: P
authors.lastname: Ellonen
authors.forename: Sakari
authors.initials: S
authors.lastname: Knuutila
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000077548:Anaplastic Lymphoma Kinase; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics*; D004252:DNA Mutational Analysis / Q000379:methods; D004311:Double-Blind Method; D005260:Female; D006801:Humans; D007150:Immunohistochemistry / Q000379:methods*; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D008175:Lung Neoplasms / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D015514:Oncogene Proteins, Fusion / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D020794:Receptor Protein-Tyrosine Kinases / Q000235:genetics*
chemical_list: D015514:Oncogene Proteins, Fusion; C000626173:ALK protein, human; D000077548:Anaplastic Lymphoma Kinase; D020794:Receptor Protein-Tyrosine Kinases