TY - JOUR
T1 - Detection of clinically actionable gene fusions by next-generation sequencing-based RNA sequencing of non–small cell lung cancer cytology specimens
T2 - A single-center experience with comparison to fluorescence in situ hybridization
AU - Diks, John
AU - Tang, Zhenya
AU - Altan, Mehmet
AU - Anderson, Sarah
AU - Chen, Hui
AU - Rashid, Asif
AU - Yang, Richard Kenneth
AU - Routbort, Mark J.
AU - Patel, Keyur P.
AU - Toruner, Gokce A.
AU - Medeiros, L. Jeffrey
AU - Tang, Guilin
AU - Luthra, Rajyalakshmi
AU - Roy-Chowdhuri, Sinchita
N1 - Publisher Copyright:
© 2023 American Cancer Society.
PY - 2024/1
Y1 - 2024/1
N2 - 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.
AB - 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.
KW - comprehensive genomic profiling (CGP)
KW - cytology specimens
KW - fluorescence in situ hybridization (FISH)
KW - gene fusions
KW - next-generation sequencing
KW - non–small cell lung cancer
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U2 - 10.1002/cncy.22766
DO - 10.1002/cncy.22766
M3 - Article
C2 - 37747438
AN - SCOPUS:85172886374
SN - 1934-662X
VL - 132
SP - 41
EP - 49
JO - Cancer Cytopathology
JF - Cancer Cytopathology
IS - 1
ER -