Intact or Broken-apart RNA. Issue 1 (January 2015)

• Record Type: Journal Article
• Authors: Kotoula, Vassiliki; Bobos, Mattheos; Vassilakopoulou, Maria; Tsolaki, Eleftheria; Chrisafi, Sofia; Psyrri, Amanda; Lazaridis, George; Papadopoulou, Kyriaki; Efstratiou, Ioannis; Michail-Strantzia, Catherine; Debelenko, Larisa V.; Kosmidis, Paris; Fountzilas, George
• Is Part Of: Applied immunohistochemistry & molecular morphology. Volume 23:Issue 1(2015)
• Publication Date: 2015-01
• Subjects: Diagnostic immunohistochemistry -- Periodicals; Immunohistochemistry -- Periodicals; Cells -- Morphology -- Periodicals; Molecular diagnosis -- Periodicals; 616.079
• DOI: 10.1097/PAI.0000000000000028
• Languages: English
• ISSNs: 1541-2016

Abstract

<abstract> <title> <x xml:space="preserve">Abstract</x> </title> <sec> <p>Anaplastic lymphoma kinase (<italic>ALK</italic>) break-apart fluorescent in situ hybridization (FISH) is currently used in diagnostics for the selection of non–small cell lung cancer (NSCLC) patients to receive crizotinib. We evaluated <italic>ALK</italic> status in NSCLC with a novel <italic>ALK</italic> mRNA test based on the break-apart FISH concept, which we called break-apart transcript (BAT) test. <italic>ALK</italic>5′ and <italic>ALK</italic>3′ transcript patterns were established with qPCR for <italic>ALK</italic>-expressing controls including fusion-negative neuroblastomas, as well as fusion-positive anaplastic large cell lymphomas and NSCLC. The BAT test was evaluated on 271 RNA samples from routinely processed paraffin NSCLC tissues. Test results were compared with ALK FISH (n=121), immunohistochemical (IHC) analysis (n=86), and automated quantitative analysis (AQUA, n=83). On the basis of the nonoverlapping <italic>ALK</italic> BAT patterns in <italic>ALK</italic>-expressing controls (<italic>P</italic><0.0001), 8/174 adenocarcinomas (4.6%) among 259 informative NSCLC were predicted as fusion positive. Overall concordance for paired method results was high (94.1% to 98.8%) but mainly concerned negative prediction because of the limited availability of positive-matched cases. Tumors with 100% cytoplasmic IHC staining of any intensity (n=3) were positive for AQUA, FISH, and BAT test; tumors with lower IHC positivity and different staining patterns were AQUA-negative. Upon multiple reevaluations, <italic>ALK</italic> gene status was considered as originally misinterpreted by FISH in 3/121 cases (2.5%). Tumors with >4 <italic>ALK</italic> gene copies were associated with longer overall survival upon first-line chemotherapy. In conclusion, application of the <italic>ALK</italic> BAT test on routinely processed NSCLC tissues yields the same fusion partner independent information as <italic>ALK</italic> break-apart FISH but is more robust and cost-effective. The BAT concept may be considered for the development of further drug-predictive translocation tests.</p> </sec> </abstract>