A single-tube multiplexed assay for detecting ALK, ROS1, and RET fusions in lung cancer

Maruja E. Lira, Yoon La Choi, Sun Min Lim, Shibing Deng, Donghui Huang, Mark Ozeck, Joungho Han, Ji Yun Jeong, Hyo Sup Shim, Byoung Chul Cho, Jhingook Kim, Myung Ju Ahn, Mao Mao

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Abstract

Approximately 7% of non-small cell lung carcinomas (NSCLCs) harbor oncogenic fusions involving ALK, ROS1, and RET. Although tumors harboring ALK fusions are highly sensitive to crizotinib, emerging preclinical and clinical data demonstrate that patients with ROS1 or RET fusions may also benefit from inhibitors targeting these kinases. Using a transcript-based method, we designed a combination of 3′ overexpression and fusion-specific detection strategies to detect ALK, ROS1 and RET fusion transcripts in NSCLC tumors. We validated the assay in 295 NSCLC specimens and showed that the assay is highly sensitive and specific. ALK results were 100% concordant with fluorescence in situ hybridization (FISH) (n = 52) and 97.8% concordant with IHC (n = 179) [sensitivity, 96.8% (95% CI 91.0%-98.9%); specificity, 98.8% (95% CI 93.6%-99.8%)]. For ROS1 and RET, we also observed 100% concordance with FISH (n = 46 and n = 15, respectively). We identified seven ROS1 and 14 RET fusion-positive tumors and confirmed the fusion status by RT-PCR and FISH. One RET fusion involved a novel partner, cutlike homeobox 1 gene (CUX1), yielding an in-frame CUX1-RET fusion. ROS1 and RET fusions were significantly enriched in tumors without KRAS/EGFR/ALK alterations. ALK/ROS1/RET/EGFR/KRAS alterations were mutually exclusive. As a single-tube assay, this test shows promise as a more practical and cost-effective screening modality for detecting rare but targetable fusions in NSCLC.

Original languageEnglish
Pages (from-to)229-243
Number of pages15
JournalJournal of Molecular Diagnostics
Volume16
Issue number2
DOIs
Publication statusPublished - 2014 Mar 1

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All Science Journal Classification (ASJC) codes

  • Pathology and Forensic Medicine
  • Molecular Medicine

Cite this

Lira, M. E., Choi, Y. L., Lim, S. M., Deng, S., Huang, D., Ozeck, M., Han, J., Jeong, J. Y., Shim, H. S., Cho, B. C., Kim, J., Ahn, M. J., & Mao, M. (2014). A single-tube multiplexed assay for detecting ALK, ROS1, and RET fusions in lung cancer. Journal of Molecular Diagnostics, 16(2), 229-243. https://doi.org/10.1016/j.jmoldx.2013.11.007