title: Native and rearranged ALK copy number and rearranged cell count in non-small cell lung cancer: implications for ALK inhibitor therapy.
abstract: BACKGROUND
  Patients with anaplastic lymphoma kinase (ALK)-positive non-small cell lung cancer (NSCLC) respond to ALK inhibitors. Clinically, the presence of ≥15% cells with rearrangements identified on break-apart fluorescence in situ hybridization (FISH) classifies tumors as positive. Increases in native and rearranged ALK copy number also occur.
  
  
  METHODS
  In total, 1426 NSCLC clinical specimens (174 ALK-positive specimens and 1252 ALK-negative specimens) and 24 ALK-negative NSCLC cell lines were investigated. ALK copy number and genomic status were assessed by FISH.
  
  
  RESULTS
  Clinical specimens with 0% to 9%, 10% to 15%, 16% to 30%, 31% to 50%, and >50% ALK-positive cells were identified in 79.3%, 8.5%, 1.4%, 2.7%, and 8.1%, respectively. An increased native ALK copy number (≥3 copies per cell in ≥40% of cells) was detected in 19% of ALK-positive tumors and in 62% of ALK-negative tumors. In ALK-negative tumors, abundant, focal amplification of native ALK was rare (0.8%). Other atypical patterns occurred in approximately 6% of tumors. The mean native ALK copy number ranged from 2.1 to 6.9 copies in cell lines and was not correlated with crizotinib sensitivity (50% inhibitory concentration, 0.34-2.8 μM; r = 0.279; P = .1764). Neither native or rearranged ALK copy number nor the percentage of positive cells correlated with extra-central nervous system progression-free survival in ALK-positive patients who were receiving crizotinib.
  
  
  CONCLUSIONS
  Overall, 8.5% of tumors fell below the established positivity threshold by ≤5%. Further investigation of ALK by other diagnostic techniques in such cases may be warranted. Native ALK copy number increases alone were not associated with sensitivity to ALK inhibition in vitro. However, rare, complex patterns of increased native ALK in patients should be studied further; because, otherwise, atypical rearrangements contained within these may be missed.
authors.affiliation: Department of Medicine, Division of Medical Oncology, University of Colorado, Denver, Colorado.
authors.forename: D Ross
authors.initials: DR
authors.lastname: Camidge
authors.forename: Margaret
authors.initials: M
authors.lastname: Skokan
authors.forename: Porntip
authors.initials: P
authors.lastname: Kiatsimkul
authors.forename: Barbara
authors.initials: B
authors.lastname: Helfrich
authors.forename: Xian
authors.initials: X
authors.lastname: Lu
authors.forename: Anna E
authors.initials: AE
authors.lastname: Barón
authors.forename: Nathan
authors.initials: N
authors.lastname: Schulte
authors.forename: DeLee
authors.initials: D
authors.lastname: Maxson
authors.forename: Dara L
authors.initials: DL
authors.lastname: Aisner
authors.forename: Wilbur A
authors.initials: WA
authors.lastname: Franklin
authors.forename: Robert C
authors.initials: RC
authors.lastname: Doebele
authors.forename: Marileila
authors.initials: M
authors.lastname: Varella-Garcia
mesh_terms: D000077548:Anaplastic Lymphoma Kinase; D002289:Carcinoma, Non-Small-Cell Lung / Q000188:drug therapy* / Q000201:enzymology* / Q000235:genetics; D045744:Cell Line, Tumor; D000077547:Crizotinib; D056915:DNA Copy Number Variations; D018572:Disease-Free Survival; D015321:Gene Rearrangement; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008175:Lung Neoplasms / Q000188:drug therapy* / Q000201:enzymology* / Q000235:genetics; D047428:Protein Kinase Inhibitors / Q000494:pharmacology*; D011720:Pyrazoles / Q000494:pharmacology; D011725:Pyridines / Q000494:pharmacology; D020794:Receptor Protein-Tyrosine Kinases / Q000037:antagonists & inhibitors* / Q000235:genetics* / Q000378:metabolism
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: anaplastic lymphoma kinase; borderline; copy number; crizotinib; florescence in situ hybridization
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