A single-tube multiplexed assay for detecting ALK, ROS1, and RET fusions in lung cancer
Maruja E Lira1, Yoon-La Choi2, Sun Min Lim3
1Oncology Research Unit, Pfizer Inc, San Diego, California.
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.
Insights
A new assay effectively detects ALK, ROS1, and RET fusions in non-small cell lung cancer (NSCLC). This sensitive and specific test aids in identifying patients who may benefit from targeted therapies.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- Approximately 7% of non-small cell lung carcinomas (NSCLCs) feature oncogenic fusions in ALK, ROS1, and RET genes.
- While ALK fusions predict response to crizotinib, emerging data suggest ROS1 and RET fusions may also respond to targeted inhibitors.
Purpose of the Study:
- To develop and validate a sensitive and specific transcript-based assay for detecting ALK, ROS1, and RET fusion transcripts in NSCLC.
- To assess the utility of this assay as a screening tool for identifying targetable fusions in NSCLC.
Main Methods:
- A novel transcript-based assay combining 3' overexpression and fusion-specific detection strategies was designed.
- The assay was validated on 295 NSCLC specimens, with results compared against fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC).
Main Results:
- The assay demonstrated high sensitivity and specificity, with 100% concordance with FISH for ALK, ROS1, and RET fusions.
- ALK results showed 97.8% concordance with IHC. Seven ROS1 and 14 RET fusion-positive tumors were identified, including a novel CUX1-RET fusion.
- ROS1 and RET fusions were enriched in tumors lacking KRAS/EGFR/ALK alterations, and these alterations were mutually exclusive.
Conclusions:
- The developed single-tube assay is a sensitive, specific, and practical method for detecting ALK, ROS1, and RET fusions in NSCLC.
- This assay holds promise as a cost-effective screening tool for identifying rare, targetable fusions, potentially guiding personalized treatment strategies.
More Related Videos
09:49Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
Published on: July 5, 2019
10:13A Multiplexed Luciferase-based Screening Platform for Interrogating Cancer-associated Signal Transduction in Cultured Cells
Published on: July 3, 2013