title: Comparison of methods in the detection of ALK and ROS1 rearrangements in lung cancer.
abstract: BACKGROUND
  The use of targeted therapies toward specific oncogenic driver mutations has become a critical factor in the treatment of patients with lung cancer. It is therefore essential to utilize tests with high performance characteristics. Fluorescence in situ hybridization (FISH) is the standard method for detecting anaplastic lymphoma kinase (ALK) and ROS1 rearrangements in non-small-cell lung cancer but the utility of other methods such as immunohistochemistry (IHC) and chromogenic in situ hybridization (CISH) is unclear.
  
  
  METHODS
  Three hundred and sixty-two lung cancer patients were tested with FISH, CISH, and IHC using three ALK antibodies (ALK1, 5A4, D5F3) and one ROS1 antibody in the detection of ALK and ROS1 rearrangements.
  
  
  RESULTS
  There was a 97.4% concordance (298 of 306) between FISH and CISH for detection of ALK rearrangements. The ROS1 rearrangement status had a 97% (291 of 300) concordance between CISH and FISH. ALK protein expression was observed in 6 of 341 samples with the ALK1 and 5A4 antibodies and 5 of 341 samples with D5F3. All three antibodies stained each of the ALK FISH-positive samples (100% sensitivity). ROS1 protein expression was observed in 2 of 322 samples. One of three samples with a ROS1 rearrangement by FISH showed ROS1 protein expression (33.3% sensitivity).
  
  
  CONCLUSIONS
  Our findings show good correlation between FISH versus CISH in the detection of ALK and ROS1 rearrangements. FISH versus IHC showed good correlation in the detection of ALK rearrangements but showed weak correlation in the detection of ROS1 rearrangements. These results suggest CISH and IHC could be complimentary detection methods to FISH in the detection of ALK and ROS1 rearrangements.
authors: *Department of Pathology, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Victoria, 3002, Australia; †Department of Anatomical Pathology, St Vincent's Hospital, Victoria Parade, Fitzroy, Victoria, 3065, Australia; ‡Department of Surgery, St Vincent's Hospital, The University of Melbourne, Victoria Parade, Fitzroy, Victoria, 3065, Australia; §Ventana Medical Systems Inc, 1910 Innovation Park Drive, Tucson, AZ 85755; and ‖Department of Haematology and Medical Oncology, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Victoria, 3002, Australia.
authors: Toni-Maree
authors: TM
authors: Rogers
authors: Prudence A
authors: PA
authors: Russell
authors: Gavin
authors: G
authors: Wright
authors: Zoe
authors: Z
authors: Wainer
authors: Jia-Min
authors: JM
authors: Pang
authors: Leigh A
authors: LA
authors: Henricksen
authors: Shalini
authors: S
authors: Singh
authors: Stacey
authors: S
authors: Stanislaw
authors: James
authors: J
authors: Grille
authors: Esteban
authors: E
authors: Roberts
authors: Benjamin
authors: B
authors: Solomon
authors: Stephen B
authors: SB
authors: Fox
mesh_terms: D000077548:Anaplastic Lymphoma Kinase; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D005260:Female; D015321:Gene Rearrangement; D006801:Humans; D007150:Immunohistochemistry; D017404:In Situ Hybridization, Fluorescence; D008175:Lung Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D008297:Male; D008875:Middle Aged; D009154:Mutation; D011505:Protein-Tyrosine Kinases / Q000235:genetics* / Q000378:metabolism; D011518:Proto-Oncogene Proteins / Q000235:genetics* / Q000378:metabolism; D020794:Receptor Protein-Tyrosine Kinases / Q000235:genetics* / Q000378:metabolism; D012189:Retrospective Studies
chemical_list: D011518:Proto-Oncogene Proteins; C000626173:ALK protein, human; D000077548:Anaplastic Lymphoma Kinase; D011505:Protein-Tyrosine Kinases; C062333:ROS1 protein, human; D020794:Receptor Protein-Tyrosine Kinases