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Rapid Multiplex RNA-Based Assay Under Study in Detection of Genetic Rearrangements and Alterations

By: Kayci Reyer
Posted: Monday, May 2, 2022

According to research presented in The Journal of Molecular Diagnostics, an ultrarapid multiplex reverse transcriptase–polymerase chain reaction (RT-PCR)-based assay may be effective in detecting NTRK1/2/3, ALK, R0S1, and RET fusions as well as MET exon 14 skipping alterations. Testing was reported to be successful in 99% of 143 tumor samples, with a demonstrated sensitivity of 81% (22 of 27 samples) for NTRK1/2/3 rearrangements. In addition, this 3-hour automated process incorporates RNA extraction, avoiding tissue losses common to independent extraction protocols.

“The assay enables rapid screening for clinically actionable kinase alterations with quicker turnaround and lower tissue requirements compared with immunohistochemistry and other molecular methods, while also circumventing the infrastructure dependencies associated with next-generation sequencing and fluorescence in situ hybridization,” stated Maria E. Arcila, MD, of Memorial Sloan Kettering Cancer Center, New York, and colleagues.

The study authors analyzed 143 independent tumor samples, 112 of which were surgical specimens and 31 were cytologic samples processed as formalin-fixed, paraffin embedded tissue preparations. Of these samples, 133 had known gene rearrangements, and 10 were negative. Testing was performed successfully on all but one sample.

In detecting NTRK1/2/3 alterations, the assay had an 81% sensitivity. As for ALK, RET, ROS1, and MET exon 14 skipping alterations, the assay had a sensitivity of 97%, 100%, 92%, and 100%, respectively. The assay was 100% specific for all expected alterations. Testing performed on samples aged a maximum of 5 years, those with greater than 10% tumor cells, those with inputs of no less than 9 mm2, and cytologic cell blocks of 9,000 cells demonstrated congruous results.

According to the study authors, “a notable advantage of the assay is the minimal tissue requirements, allowing the concurrent performance of both DNA and RNA assays in limited samples.” Other benefits of the novel assay include algorithmic interpretation of multichannel fluorescent outputs and the performance of single patient testing on demand without the need for batching. Further pipeline adjustments that are tumor specific are in progress, which may improve the sensitivity of NTRK1/2/3 alteration calling.

Disclosure: For full disclosures of the study authors, visit jmdjournal.org.


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