title: Identification ofALK,ROS1, andRETFusions by a Multiplexed mRNA-Based Assay in Formalin-Fixed, Paraffin-Embedded Samples from Advanced Non-Small-Cell Lung Cancer Patients.
abstract: Anaplastic lymphoma receptor tyrosine kinase (ALK), ROS proto-oncogene 1, receptor tyrosine kinase (ROS1), and ret proto-oncogene (RET) fusions are present in 5%-7% of patients with advanced non-small-cell lung cancer (NSCLC); their accurate identification is critical to guide targeted therapies. FISH and immunohistochemistry (IHC) are considered the gold standards to determine gene fusions, but they have limitations. The nCounter platform is a potentially useful genomic tool for multiplexed detection of gene fusions, but has not been validated in the clinical setting.
  
  
  
  Formalin-fixed, paraffin embedded (FFPE) samples from 108 patients with advanced NSCLC were analyzed with an nCounter-based assay and the results compared with FISH, IHC, and reverse transcription PCR (RT-PCR). Data on response to fusion kinase inhibitors was retrospectively collected in a subset of 29 patients.
  
  
  
  Of 108 FFPE samples, 98 were successfully analyzed by nCounter (91%), which identified 55 fusion-positive cases (32ALK, 21ROS1, and 2RET). nCounter results were highly concordant with IHC for ALK (98.5%, CI = 91.8-99.7), while 11 discrepancies were found compared with FISH (87.5% concordance, CI = 79.0-92.9). ForROS1, nCounter showed similar agreement with IHC and FISH (87.2% and 85.9%), but a substantial number of samples were positive only by 1 or 2 techniques. Of the 25 patients deriving clinical benefit from fusion kinase inhibitors, 24 were positive by nCounter and 22 by FISH.
  
  
  
  nCounter compares favorably with IHC and FISH and can be used for identifying patients with advanced NSCLC positive forALK/ROS1/RETfusion genes.
authors.affiliation: Medical Oncology, Hospital Clínic, Barcelona, Spain; nreguart@clinic.ub.es mamolina@pangaeabiotech.com.|Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
authors.forename: Noemí
authors.initials: N
authors.lastname: Reguart
authors.affiliation: Pangaea Biotech, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain.
authors.forename: Cristina
authors.initials: C
authors.lastname: Teixidó
authors.affiliation: Pangaea Biotech, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain.
authors.forename: Ana
authors.initials: A
authors.lastname: Giménez-Capitán
authors.affiliation: Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
authors.forename: Laia
authors.initials: L
authors.lastname: Paré
authors.affiliation: Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.|Pangaea Biotech, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain.|Translational Genomics Group, Vall d'Hebron Institute of Oncology (VHIO).
authors.forename: Patricia
authors.initials: P
authors.lastname: Galván
authors.affiliation: Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain.
authors.forename: Santiago
authors.initials: S
authors.lastname: Viteri
authors.affiliation: Pangaea Biotech, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain.
authors.forename: Sonia
authors.initials: S
authors.lastname: Rodríguez
authors.affiliation: Pangaea Biotech, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain.
authors.forename: Vicente
authors.initials: V
authors.lastname: Peg
authors.affiliation: Pangaea Biotech, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain.
authors.forename: Erika
authors.initials: E
authors.lastname: Aldeguer
authors.affiliation: Medical Oncology, Hospital Clínic, Barcelona, Spain.
authors.forename: Nuria
authors.initials: N
authors.lastname: Viñolas
authors.affiliation: Department of Medical Oncology, Gustave Roussy, Université Paris-Saclay, Villejuif, France.
authors.forename: Jordi
authors.initials: J
authors.lastname: Remon
authors.affiliation: Pangaea Biotech, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain.|Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain.|University Hospital Sagrat Cor, Barcelona, Spain.
authors.forename: Niki
authors.initials: N
authors.lastname: Karachaliou
authors.affiliation: Laboratorio de Dianas Terapéuticas, Centro Integral Oncológico Clara Campal, Hospital Universitario Madrid Sanchinarro, Madrid, Spain.
authors.forename: Esther
authors.initials: E
authors.lastname: Conde
authors.affiliation: Laboratorio de Dianas Terapéuticas, Centro Integral Oncológico Clara Campal, Hospital Universitario Madrid Sanchinarro, Madrid, Spain.
authors.forename: Fernando
authors.initials: F
authors.lastname: Lopez-Rios
authors.affiliation: Medical Oncology Service, Catalan Institute of Oncology, L'Hospitalet, Spain.
authors.forename: Ernest
authors.initials: E
authors.lastname: Nadal
authors.affiliation: Institute of Pathology, University Hospital Cologne, Cologne, Germany.
authors.forename: Sabine
authors.initials: S
authors.lastname: Merkelbach-Bruse
authors.affiliation: Institute of Pathology, University Hospital Cologne, Cologne, Germany.
authors.forename: Reinhard
authors.initials: R
authors.lastname: Büttner
authors.affiliation: Pangaea Biotech, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain.|Dr Rosell Oncology Institute, Quirón Dexeus University Hospital, Barcelona, Spain.|Cancer Biology and Precision Medicine Program, Catalan Institute of Oncology, Germans Trias i Pujol Health Sciences Institute and Hospital, Badalona, Barcelona, Spain.
authors.forename: Rafael
authors.initials: R
authors.lastname: Rosell
authors.affiliation: Pangaea Biotech, Laboratory of Oncology, Quirón Dexeus University Hospital, Barcelona, Spain; nreguart@clinic.ub.es mamolina@pangaeabiotech.com.
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Molina-Vila
authors.affiliation: Medical Oncology, Hospital Clínic, Barcelona, Spain.|Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
authors.forename: Aleix
authors.initials: A
authors.lastname: Prat
mesh_terms: D000077548:Anaplastic Lymphoma Kinase; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics*; D045744:Cell Line, Tumor; D005557:Formaldehyde; D006801:Humans; D007150:Immunohistochemistry; D017404:In Situ Hybridization, Fluorescence; D008175:Lung Neoplasms / Q000235:genetics; D015514:Oncogene Proteins, Fusion / Q000235:genetics*; D016612:Paraffin Embedding; D011505:Protein-Tyrosine Kinases / Q000235:genetics* / Q000378:metabolism; D000090063:Proto-Oncogene Mas; D011518:Proto-Oncogene Proteins / Q000235:genetics* / Q000378:metabolism; D051096:Proto-Oncogene Proteins c-ret / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000032:analysis* / Q000235:genetics; D020794:Receptor Protein-Tyrosine Kinases / Q000235:genetics* / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016707:Tissue Fixation
chemical_list: C000715470:MAS1 protein, human; D015514:Oncogene Proteins, Fusion; D000090063:Proto-Oncogene Mas; D011518:Proto-Oncogene Proteins; D012333:RNA, Messenger; D005557:Formaldehyde; C000626173:ALK protein, human; D000077548:Anaplastic Lymphoma Kinase; D011505:Protein-Tyrosine Kinases; D051096:Proto-Oncogene Proteins c-ret; C062333:ROS1 protein, human; D020794:Receptor Protein-Tyrosine Kinases