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Updated: Jul 30, 2025
Author Spotlight: Advancements in Molecular Biomarker Testing for Non-Squamous Non-Small Cell Lung Cancer
Published on: September 8, 2023
Gene Fusion Detection in NSCLC Routine Clinical Practice: Targeted-NGS or FISH?
Lorenza Pecciarini1, Emanuela Brunetto1, Greta Grassini1
1Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy.
Abstract:
The ability to identify the broadest range of targetable gene fusions is crucial to facilitate personalized therapy selection for advanced lung adenocarcinoma (LuADs) patients harboring targetable receptor tyrosine kinase (RTK) genomic alterations. In order to evaluate the most effective testing approach for LuAD targetable gene fusion detection, we analyzed 210 NSCLC selected clinical samples, comparing in situ (Fluorescence In Situ Hybridization, FISH, and ImmunoHistoChemistry, IHC) and molecular (targeted RNA Next-Generation Sequencing, NGS, and RealTime-PCR, RT-PCR) approaches. The overall concordance among these methods was high (>90%), and targeted RNA NGS was confirmed to be the most efficient technique for gene fusion identification in clinical practice, allowing the simultaneous analysis of a large set of genomic rearrangements at the RNA level. However, we observed that FISH was useful to detect targetable fusions in those samples with inadequate tissue material for molecular testing as well as in those few cases whose fusions were not identified by the RNA NGS panel. We conclude that the targeted RNA NGS analysis of LuADs allows accurate RTK fusion detection; nevertheless, standard methods such as FISH should not be dismissed, as they can crucially contribute to the completion of the molecular characterization of LuADs and, most importantly, the identification of patients as candidates for targeted therapies.
Insights
Targeted RNA Next-Generation Sequencing (NGS) is the most efficient method for detecting gene fusions in lung adenocarcinoma (LuAD). Fluorescence In Situ Hybridization (FISH) remains valuable for confirming results and analyzing limited tissue samples.
Area of Science:
- Oncology
- Genomics
- Molecular Diagnostics
Background:
- Accurate identification of targetable gene fusions is critical for personalized therapy in advanced lung adenocarcinoma (LuAD).
- Receptor tyrosine kinase (RTK) genomic alterations are key targets for precision medicine in LuAD patients.
Purpose of the Study:
- To evaluate and compare the effectiveness of different testing approaches for detecting targetable gene fusions in LuAD.
- To determine the optimal molecular diagnostic strategy for LuAD patients with RTK alterations.
Main Methods:
- Analysis of 210 non-small cell lung cancer (NSCLC) clinical samples.
- Comparison of in situ methods (Fluorescence In Situ Hybridization [FISH], Immunohistochemistry [IHC]) with molecular methods (targeted RNA Next-Generation Sequencing [NGS], Real-Time PCR [RT-PCR]).
Main Results:
- High overall concordance (>90%) was observed among the tested methods.
- Targeted RNA NGS demonstrated superior efficiency for broad gene fusion identification at the RNA level.
- FISH proved useful for samples with insufficient tissue for molecular testing and for confirming rare fusion findings.
Conclusions:
- Targeted RNA NGS is highly accurate for RTK fusion detection in LuAD.
- Standard methods like FISH are essential for comprehensive molecular characterization and patient identification for targeted therapies.
- A combined approach may be optimal for maximizing diagnostic yield in LuAD.
