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Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
Published on: July 5, 2019
NTRK Gene Fusion Detection in a Pan-Cancer Setting Using the Idylla GeneFusion Assay
Laure Sorber1, Bieke Van Dorst2, Ellen Bellon2
1Center for Oncological Research, Integrated Personalized and Precision Oncology Network, University of Antwerp, Wilrijk, Belgium.
Abstract:
Recently, approval of tyrosine receptor kinase (TRK) inhibitors by Food and Drug Administration and European Medicines Agency in NTRK fusion-positive cancer types has led to a variety of proposed testing algorithms. In this study, performance of the fully automated Idylla GeneFusion Assay was assessed in a set of clinically relevant cancer types, including glioblastoma, non-small-cell lung cancer, microsatellite instability-positive colorectal cancer, and thyroid carcinoma. Analysis with the Idylla GeneFusion Assay revealed significant differences in baseline RNA expression profile between the different cancer types, which corresponded to both literature and pan-TRK immunohistochemical staining. Compared with the RNA-based Oncomine Focus Assay, the Idylla GeneFusion Assay demonstrated an overall percentage agreement, positive percentage agreement, and negative percentage agreement of 92.7%, 81.8%, and 93.8%, respectively; and the pan-TRK immunohistochemistry demonstrated an overall percentage agreement, positive percentage agreement, and negative percentage agreement of 82.1%, 45.5%, and 85.7%, respectively. These findings highlighted the importance of tailoring NTRK testing algorithms per cancer type. In a small subset, data from the RNA-based Archer FusionPlex Assay were also available. NTRK fusion detection efficiency was compared between the four NTRK testing modalities, with a high concordance between the PCR-based methods. Last, RNA degradation was observed when using the Idylla GeneFusion Assay on snap frozen tissue samples as these are nonfixated. This might be countered by increasing the amount of sample input. To conclude, the Idylla GeneFusion Assay has shown a clear potential in identifying NTRK fusions.
Insights
The Idylla GeneFusion Assay shows potential for identifying NTRK fusions in various cancers. Tailoring testing algorithms per cancer type is crucial for accurate results, especially with RNA degradation concerns in frozen samples.
Area of Science:
- Oncology
- Molecular Diagnostics
- Genetics
Background:
- The approval of tyrosine receptor kinase (TRK) inhibitors necessitates reliable testing for NTRK fusions in cancer patients.
- Various testing algorithms are proposed, highlighting the need to evaluate their performance across different cancer types.
Purpose of the Study:
- To assess the performance of the fully automated Idylla GeneFusion Assay for detecting NTRK fusions.
- To compare the Idylla GeneFusion Assay with other methods like Oncomine Focus Assay and pan-TRK immunohistochemistry.
- To investigate the impact of cancer type on RNA expression profiles and NTRK fusion detection.
Main Methods:
- The Idylla GeneFusion Assay was evaluated on clinically relevant cancer types: glioblastoma, non-small-cell lung cancer, colorectal cancer, and thyroid carcinoma.
- Performance was compared against the RNA-based Oncomine Focus Assay and pan-TRK immunohistochemistry.
- NTRK fusion detection efficiency was also compared with the Archer FusionPlex Assay in a subset of samples.
Main Results:
- The Idylla GeneFusion Assay demonstrated high overall agreement (92.7%) with the Oncomine Focus Assay, with specific agreements of 81.8% positive and 93.8% negative.
- Pan-TRK immunohistochemistry showed lower agreement (82.1% overall, 45.5% positive, 85.7% negative) compared to RNA-based assays.
- Significant differences in baseline RNA expression were observed between cancer types, influencing testing outcomes. RNA degradation was noted in snap-frozen samples.
- High concordance was observed between PCR-based methods (Idylla and Archer FusionPlex).
Conclusions:
- The Idylla GeneFusion Assay is a promising tool for NTRK fusion detection.
- Tailoring NTRK testing algorithms based on cancer type is essential for clinical utility.
- Addressing RNA degradation in frozen samples, possibly by increasing input, is important for assay reliability.
