New study suggests RT-PCR-based ALK assay useful in clinical practice

Anaplastic lymphoma kinase (ALK) gene rearrangements are found in 3–5% of lung adenocarcinomas (ADC) (2–4, Figure 1), and over 20 ALK fusion partners have been implicated in non-small-cell lung cancer (NSCLC) (5). Thanks to the relatively recent development of small molecule targeted therapies, the ALK oncogene is now targetable using ALK tyrosine kinase inhibitors (TKIs) (6, 7). Identification of ALK alterations is essential to selecting patients for such treatments (4, 6, 11, 12, Figure 2).

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Figure 1. Frequency of genomic alterations in lung adenocarcinoma. (click on image to enlarge)

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Figure 2. ALK testing is required for treatment with ALK TKIs. (click on image to enlarge)

A sensitive and specific method for the identification of ALK rearrangements is RT-PCR of cDNA (8, 9). A recent technical validation study by Marchetti et al. (10) evaluates a new algorithm for a quick and easy RT-PCR-based ALK assay to establish the ALK status in a large cohort of lung ADC patients. The Marchetti study compares an RT-PCR-based ALK detection assay with two standard laboratory methods for to screening and selection of patients for ALK inhibitors, FISH and IHC. The study,  performed by the Center for Excellence on Ageing and Translational Medicine (CeSI-MeT) at the University of Chieti in Italy, tested samples from small biopsies with tissue alterations, collected by electrosurgical machines. Researchers first ran a pilot series by testing 100 samples (13 +ve), followed by a validation series, by testing 117 samples (15 +ve). In both the pilot and validation series, results from the the ALK RT-PCR assay showed 100% concordance with FISH. Of the 28 +ve samples (FISH/ALK RT-PCR), 2 samples scored –ve by IHC.

Through comparing the data generated from RT-PC-based ALK assay with data generated using FISH, IHC and NGS, Marchetti et al. validate the RT-PCR-based assay by demonstrating 100% sensitivity and specificity of this assay when compared to FISH as a standard. These results demonstrate that an RT-PCR-based ALK assay could be useful clinical practice to determine ALK status as a complementary assay in multi-test diagnostic algorithms. In addition, this type of RT-PCR-based ALK assay was shown to have benefits versus FISH as the gold standard method. The ALK FISH assay, currently used as the standard of care, is known to have technical challenges, including FISH signal instability and scoring difficulties (16). The limitations of diagnosis with FISH have been well described (13–15), supporting the need for reconsideration of the diagnostic screening method for ALK inhibitors. By comparing an RT-PCR-based assay to FISH, Marchetti eta al. described the RT-PCR ALK assay as a simple and rapid test sensitive enough to be applicable to small biopsies. Pending confirmation from independent studies, the Marchetti study concludes that a RT-PCR-based ALK assay could potentially be used as a reliable standalone test for the selection of ALK positive samples, and as a screening test for patients to be treated with ALK inhibitors.

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References:

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    2. 2. Shaw, A.T., et al. (2009) Clinical features and outcome of patients with non-small-cell lung cancer who harbor EML4-ALK. J Clin Oncol. 27(26):4247–4253. Link
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    4. 4. Chiarle, R., et al. (2008) The anaplastic lymphoma kinase in the pathogenesis of cancer. Nat Rev Cancer. 8(1):11–23. (Link)
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    11. 11. Shaw, A.T., et al. (2011) Effect of crizotinib on overall survival in patients with advanced non-small-cell lung cancer harbouring ALK gene rearrangement: a retrospective analysis. Lancet Oncol.12:1004–1012. (Link)
    12. 12. Koivunen, J.P., et al. (2008) EML4-ALK fusion gene and efficacy of an ALK kinase inhibitor in lung cancer. Clin Cancer Res.14:4275–4283. (Link)
    13. 13. Rodig, S.J., et al. (2009) Unique clinicopathologic features characterize ALK-rearranged lung adenocarcinoma in the western population. Clin Cancer Res 15:5216–23. (Link)
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    15. 15. Sholl L.M., et al. (2013) Combined use of ALK immunohistochemistry and FISH for optimal detection of ALK-rearranged lung adenocarcinomas. J Thorac Oncol 8(3):322–328. (Link)
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Kathryn Collinet

Kathryn Collinet, PhD, is a Technical and Marketing Writer for Personalized Healthcare and Oncology at QIAGEN. She trained as a molecular biologist at the University of Barcelona and the Institute for Research in Biomedicine, where she studied DNA and protein modifications and their influence on chromatin conformation and gene expression. Since 2011 Kathryn has been working in marketing communications for the scientific information and molecular diagnostics industries. Kathryn has a passion for delivering knowledge and insights about molecular and clinical technologies, and their power to impact research and healthcare.

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