Ultrafast Gene Fusion Assessment for Nonsquamous NSCLC

Abstract

Introduction: Gene fusion testing of ALK, ROS1, RET, NTRK, and MET exon 14 skipping mutations is guideline recommended in nonsquamous NSCLC (NS-NSCLC). Nevertheless, assessment is often hindered by the limited availability of tissue and prolonged next-generation sequencing (NGS) testing, which can protract the initiation of a targeted therapy. Therefore, the development of faster gene fusion assessment is critical for optimal clinical decision-making. Here, we compared two ultrafast gene fusion assays (UFGFAs) using NGS (Genexus, Oncomine Precision Assay, Thermo Fisher Scientific) and a multiplex reverse-transcriptase polymerase chain reaction (Idylla, GeneFusion Assay, Biocartis) approach at diagnosis in a retrospective series of 195 NS-NSCLC cases and five extrapulmonary tumors with a known NTRK fusion.

Methods: A total of 195 NS-NSCLC cases (113 known gene fusions and 82 wild-type tumors) were included retrospectively. To validate the detection of a NTRK fusion, we added five NTRK-positive extrathoracic tumors. The diagnostic performance of the two UFGFAs and standard procedures was compared.

Results: The accuracy was 92.3% and 93.1% for Idylla and Genexus, respectively. Both systems improved the sensitivity for detection by including a 5'-3' imbalance analysis. Although detection of ROS1, MET exon 14 skipping, and RET was excellent with both systems, ALK fusion detection was reduced with sensitivities of 87% and 88%, respectively. Idylla had a limited sensitivity of 67% for NTRK fusions, in which only an imbalance assessment was used.

Conclusions: UFGFA using NGS and reverse-transcriptase polymerase chain reaction approaches had an equal level of detection of gene fusion but with some technique-specific limitations. Nevertheless, UFGFA detection in routine clinical care is feasible with both systems allowing faster initiation of therapy and a broad degree of screening.

Keywords: Gene fusion; Next generation sequencing; Non–small cell lung carcinoma; RT-PCR.

Figure 1

Testing of different populations using the Idylla qPCR system (inner ring) and the Genexus NGS system (outer ring). The numbers in parentheses are the case numbers with the alterations or percentages. qPCR, quantitative polymerase chain reaction; NGS, next-generation sequencing.

Figure 2

Detection of gene fusions using ultrafast gene fusion assays. (A) The result based on standard procedure is highlighted on the top. Each column represents one case, and each result for the respective genes analyzed using both systems is highlighted. (B) Description of gene fusion events. Results from the Genexus NGS system on the distribution of gene fusion events for each of the respective genes. Gene fusions that are not part of the Idylla design and consequently cannot be detected by the respective devices are highlighted in bold. The numbers in parentheses are the case numbers with the alterations or percentages. FISH, fluorescence in situ hybridization; IHC, immunohistochemistry; qPCR, quantitative polymerase chain reaction; NGS, next-generation sequencing.