Detection of clinically actionable gene fusions by next-generation sequencing-based RNA sequencing of non-small cell lung cancer cytology specimens: A single-center experience with comparison to fluorescence in situ hybridization.

Autor: Diks J; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA., Tang Z; Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA., Altan M; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA., Anderson S; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA., Chen H; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA., Rashid A; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA., Yang RK; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA., Routbort MJ; Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA., Patel KP; Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA., Toruner GA; Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA., Medeiros LJ; Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA., Tang G; Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA., Luthra R; Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA., Roy-Chowdhuri S; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
Jazyk: angličtina
Zdroj: Cancer cytopathology [Cancer Cytopathol] 2024 Jan; Vol. 132 (1), pp. 41-49. Date of Electronic Publication: 2023 Sep 25.
DOI: 10.1002/cncy.22766
Abstrakt: Background: Genomic profiling is needed to identify actionable alterations in non-small cell lung cancer (NSCLC). Panel-based testing such as next-generation sequencing (NGS) is often preferred to interrogate multiple alterations simultaneously. In this study, we evaluate the utility of an RNA-based NGS assay to detect genomic alterations in NSCLC cytology specimens and compare these results to fluorescence in situ hybridization (FISH) testing.
Methods: A retrospective review was performed of 264 NSCLC cytology specimens that were concurrently tested for gene fusions by RNA-based NGS and ALK, RET, and/or ROS1 by FISH.
Results: Genomic alterations were detected in 29 cases by NGS, including ALK, RET, ROS1, NTRK, NUTM1, and FGFR3 fusions and MET exon 14 skipping alterations. Of the 20 cases with ALK, RET, and ROS1 fusions detected by NGS, 16 (80%) were concordant with the corresponding FISH results. Three cases showed discordance, where EML4::ALK (n = 2) and SLC34A2::ROS1 (n = 1) fusions were not detected by the corresponding FISH assay; one case with EZR::ROS1 was inadequate for FISH. No gene fusions were detected in 181 cases by NGS and 54 cases failed testing. The concordance rates for detecting ALK, RET, and ROS1 fusions using NGS and FISH were 97%, 100%, and 99.5%, respectively.
Conclusion: RNA-based NGS can be used to detect gene fusions in NSCLC cytology cases with high concordance with FISH results. However, RNA-based NGS may have high failure rates and therefore a low threshold for reflexing inadequate cases to an orthogonal testing method is essential for comprehensive genomic profiling.
(© 2023 American Cancer Society.)
Databáze: MEDLINE
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