title: Clinical Validation of a Novel Commercial Reverse Transcription-Quantitative Polymerase Chain Reaction Screening Assay for Detection of ALK Translocations and Amplifications in Non-Small Cell Lung Carcinomas.
abstract: BACKGROUND
  -EGFR mutations and anaplastic lymphoma kinase (ALK) translocations have significant biologic and therapeutic implications in lung cancers, particularly lung adenocarcinomas. ALK translocations are less frequent compared with EGFR mutations; interestingly, these two abnormalities are most commonly mutually exclusive. The 2013 College of American Pathologists/Association for Molecular Pathology/International Association for the Study of Lung Cancer molecular testing guideline for lung cancers recommend a testing algorithm in which detection of ALK translocations using fluorescence in situ hybridization (FISH) is to be performed following testing for EGFR mutations. Such an algorithm is cost-effective but potentially slows down turnaround time; and as a secondary test, ALK FISH assay may not be completed because it requires the use of additional tissue, and the small biopsies or cytology specimens may have been exhausted in the extraction of nucleic acid for EGFR mutation screening.
  
  
  OBJECTIVE
  -To provide efficient testing of both EGFR and ALK genetic alterations in small biopsies and cytology specimens.
  
  
  METHODS
  -We validated a highly sensitive ALK reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assay as a screening tool for ALK translocations and amplifications.
  
  
  RESULTS
  -We performed a retrospective review of cases previously tested by FISH and found that all FISH ALK translocation-positive specimens were RT-qPCR positive, and all FISH ALK translocation-negative cases were RT-qPCR negative (the sensitivity and specificity of the ALK RT-qPCR assay were 100%).
  
  
  CONCLUSIONS
  -This assay allows rapid identification of ALK alterations, can be performed in conjunction with EGFR testing, and does not require use of valuable additional tumor tissue.
authors.affiliation: From the Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas. Dr Portier is now with Roche Tissue Diagnostics/Ventana Medical Systems (ROCHE Group), Tucson, Arizona.
authors.forename: Chunyan
authors.initials: C
authors.lastname: Liu
authors.forename: Kristi
authors.initials: K
authors.lastname: Pepper
authors.forename: Heather
authors.initials: H
authors.lastname: Hendrickson
authors.forename: Philip T
authors.initials: PT
authors.lastname: Cagle
authors.forename: Bryce P
authors.initials: BP
authors.lastname: Portier
mesh_terms: D000077548:Anaplastic Lymphoma Kinase; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics* / Q000473:pathology; D045744:Cell Line, Tumor; D066246:ErbB Receptors / Q000235:genetics; D005784:Gene Amplification; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics* / Q000473:pathology; D020794:Receptor Protein-Tyrosine Kinases / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D014178:Translocation, Genetic
chemical_list: C000626173:ALK protein, human; D000077548:Anaplastic Lymphoma Kinase; D066246:ErbB Receptors; D020794:Receptor Protein-Tyrosine Kinases