title: Automation of ALK gene rearrangement testing with fluorescence in situ hybridization (FISH): a feasibility study.
abstract: In the past several years we have observed a significant increase in our understanding of molecular mechanisms that drive lung cancer. Specifically in the non-small cell lung cancer sub-types, ALK gene rearrangements represent a sub-group of tumors that are targetable by the tyrosine kinase inhibitor Crizotinib, resulting in significant reductions in tumor burden. Phase II and III clinical trials were performed using an ALK break-apart FISH probe kit, making FISH the gold standard for identifying ALK rearrangements in patients. FISH is often considered a labor and cost intensive molecular technique, and in this study we aimed to demonstrate feasibility for automation of ALK FISH testing, to improve laboratory workflow and ease of testing. This involved automation of the pre-treatment steps of the ALK assay using various protocols on the VP 2000 instrument, and facilitating automated scanning of the fluorescent FISH specimens for simplified enumeration on various backend scanning and analysis systems. The results indicated that ALK FISH can be automated. Significantly, both the Ikoniscope and BioView system of automated FISH scanning and analysis systems provided a robust analysis algorithm to define ALK rearrangements. In addition, the BioView system facilitated consultation of difficult cases via the internet.
authors.affiliation: Antwerp University Hospital, Department of Pathology, Wilrijkstraat 10, 2650 Edegem, Belgium. Electronic address: Karen.Zwaenepoel@uza.be.
authors.forename: Karen
authors.initials: K
authors.lastname: Zwaenepoel
authors.affiliation: Abbott Molecular, Max-Planck-Ring 2, 65205 Wiesbaden, Germany.
authors.forename: Dennis
authors.initials: D
authors.lastname: Merkle
authors.affiliation: University of Rennes 1, Faculty of Medicine, Service de Cytogénétique et Biologie Cellulaire, CHU de Rennes, rue Henri Le Guilloux, 35033 Rennes CEDEX 9, France.
authors.forename: Florian
authors.initials: F
authors.lastname: Cabillic
authors.affiliation: Charite University Hospital Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany.
authors.forename: Erica
authors.initials: E
authors.lastname: Berg
authors.affiliation: University of Rennes 1, Faculty of Medicine, Service de Cytogénétique et Biologie Cellulaire, CHU de Rennes, rue Henri Le Guilloux, 35033 Rennes CEDEX 9, France.
authors.forename: Marc-Antoine
authors.initials: MA
authors.lastname: Belaud-Rotureau
authors.affiliation: Italian Center of Diagnostics, Laboratory of Molecular Biology and Genetics, Via Saint Bon 20, 20147 Milan, Italy.
authors.forename: Vittorio
authors.initials: V
authors.lastname: Grazioli
authors.affiliation: Abbott Molecular, Rue de la Couture 12, 94518 Rungis, France.
authors.forename: Olga
authors.initials: O
authors.lastname: Herelle
authors.affiliation: Charite University Hospital Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Hummel
authors.affiliation: University of Rennes 1, Faculty of Medicine, Service de Cytogénétique et Biologie Cellulaire, CHU de Rennes, rue Henri Le Guilloux, 35033 Rennes CEDEX 9, France.
authors.forename: Michele
authors.initials: M
authors.lastname: Le Calve
authors.affiliation: Charite University Hospital Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany.
authors.forename: Dido
authors.initials: D
authors.lastname: Lenze
authors.affiliation: Charite University Hospital Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200 Berlin, Germany.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Mende
authors.affiliation: Antwerp University Hospital, Department of Pathology, Wilrijkstraat 10, 2650 Edegem, Belgium.
authors.forename: Patrick
authors.initials: P
authors.lastname: Pauwels
authors.affiliation: Biomnis Laboratory, Laboratory of Cytogenetics, 17-19 av Tony Garnier, 69357 Lyon, France.
authors.forename: Benoit
authors.initials: B
authors.lastname: Quilichini
authors.affiliation: Italian Center of Diagnostics, Laboratory of Molecular Biology and Genetics, Via Saint Bon 20, 20147 Milan, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Repetti
mesh_terms: D000465:Algorithms; D000077548:Anaplastic Lymphoma Kinase; D001331:Automation; D002289:Carcinoma, Non-Small-Cell Lung / Q000188:drug therapy / Q000235:genetics* / Q000473:pathology; D017322:Clinical Trials, Phase II as Topic; D017326:Clinical Trials, Phase III as Topic; D000077547:Crizotinib; D003627:Data Interpretation, Statistical; D005240:Feasibility Studies; D015321:Gene Rearrangement; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D008175:Lung Neoplasms / Q000188:drug therapy / Q000235:genetics* / Q000473:pathology; D009367:Neoplasm Staging; D011379:Prognosis; D047428:Protein Kinase Inhibitors / Q000627:therapeutic use; D011720:Pyrazoles / Q000627:therapeutic use; D011725:Pyridines / Q000627:therapeutic use; D020794:Receptor Protein-Tyrosine Kinases / Q000235:genetics*; D012984:Software
chemical_list: D047428:Protein Kinase Inhibitors; D011720:Pyrazoles; D011725:Pyridines; D000077547:Crizotinib; C000626173:ALK protein, human; D000077548:Anaplastic Lymphoma Kinase; D020794:Receptor Protein-Tyrosine Kinases
keywords: ALK; Automation; BioView; FISH; Fluorescence in situ hybridization; VP 2000