Targeted RNA-sequencing assays: a step forward compared to FISH and IHC techniques?
Gaëlle Tachon1,2,3, Ulrich Cortes3, Sophie Richard2,4
1Laboratoire de Neurosciences Expérimentales et Cliniques, Inserm U1084, Poitiers, France.
Cancer Medicine
|October 26, 2019
Summary
RNA-sequencing accurately detects ALK and ROS1 rearrangements in non-small cell lung cancer, offering a viable alternative to standard IHC and FISH methods for therapy management.
Area of Science:
- Oncology
- Molecular Diagnostics
- Genomics
Background:
- Anaplastic Lymphoma Kinase (ALK) and ROS1 rearrangements are key molecular targets for tyrosine kinase inhibitors in cancer therapy.
- RNA-sequencing is emerging as a powerful tool for detecting fusion genes, presenting an alternative to conventional immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH).
Purpose of the Study:
- To compare the diagnostic accuracy of two amplicon-based RNA-sequencing kits (Archer® and Qiagen®) for detecting ALK and ROS1 rearrangements.
- To assess the utility of RNA-sequencing for therapy management in non-small cell lung cancer (NSCC).
Main Methods:
- RNA-sequencing analysis was performed on 37 formalin-fixed paraffin-embedded (FFPE) NSCC samples previously tested by IHC and FISH.
- Two kits, FusionPlex® Alk Ret Ros1 v2 Kit (Archer®) and FHS-003Z-12-Human Lung Cancer Panel (Qiagen®), were evaluated.
Main Results:
- Both Archer® and Qiagen® kits demonstrated high accuracy in identifying ALK and ROS1 rearrangements, correctly classifying 85.1% and 81.5% of positive samples, respectively.
- All negative samples (100%) were correctly identified by both RNA-sequencing kits.
- RNA-sequencing resolved 75% of ambiguous IHC-positive/FISH-negative cases, confirming FISH conclusions in most instances.
Conclusions:
- RNA-sequencing is a feasible and accurate method for detecting ALK and ROS1 rearrangements in FFPE NSCC samples.
- The evaluated RNA-sequencing kits (Archer® and Qiagen®) show comparable performance in terms of time, cost, and outcomes.
- RNA-sequencing can serve as both an alternative and a supplementary technique to IHC and FISH, particularly for classifying discrepant cases and guiding therapy decisions.
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