Related Experiment Video
Updated: Nov 16, 2025
Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
Published on: July 5, 2019
Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation
Carina Heydt1, Christina B Wölwer2, Oscar Velazquez Camacho2
1Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany. carina.heydt@uk-koeln.de.
Background:
Gene fusions represent promising targets for cancer therapy in lung cancer. Reliable detection of multiple gene fusions is therefore essential.
Methods:
Five commercially available parallel sequencing assays were evaluated for their ability to detect gene fusions in eight cell lines and 18 FFPE tissue samples carrying a variety of known gene fusions. Four RNA-based assays and one DNA-based assay were compared; two were hybrid capture-based, TruSight Tumor 170 Assay (Illumina) and SureSelect XT HS Custom Panel (Agilent), and three were amplicon-based, Archer FusionPlex Lung Panel (ArcherDX), QIAseq RNAscan Custom Panel (Qiagen) and Oncomine Focus Assay (Thermo Fisher Scientific).
Results:
The Illumina assay detected all tested fusions and showed the smallest number of false positive results. Both, the ArcherDX and Qiagen panels missed only one fusion event. Among the RNA-based assays, the Qiagen panel had the highest number of false positive events. The Oncomine Focus Assay (Thermo Fisher Scientific) was the least adequate assay for our purposes, seven fusions were not covered by the assay and two fusions were classified as uncertain. The DNA-based SureSelect XT HS Custom Panel (Agilent) missed three fusions and nine fusions were only called by one software version. Additionally, many false positive fusions were observed.
Conclusions:
In summary, especially RNA-based parallel sequencing approaches are potent tools for reliable detection of targetable gene fusions in clinical diagnostics.
Insights
This study evaluated five gene fusion detection assays for lung cancer. RNA-based parallel sequencing assays are effective for reliable clinical diagnostics of targetable gene fusions.
Area of Science:
- Molecular Oncology
- Genomics
- Cancer Diagnostics
Background:
- Gene fusions are crucial therapeutic targets in lung cancer.
- Accurate detection of multiple gene fusions is essential for effective cancer treatment.
Purpose of the Study:
- To evaluate the performance of five commercial parallel sequencing assays for detecting gene fusions.
- To compare RNA-based and DNA-based assays in identifying known gene fusions in various samples.
Main Methods:
- Comparison of five commercially available parallel sequencing assays (four RNA-based, one DNA-based).
- Assays included hybrid capture and amplicon-based methods.
- Evaluation performed on eight cell lines and 18 FFPE tissue samples with known gene fusions.
Main Results:
- The Illumina assay demonstrated high sensitivity and specificity, detecting all fusions with minimal false positives.
- ArcherDX and Qiagen panels showed high accuracy, missing only one fusion event each.
- The Thermo Fisher Scientific assay had limitations in fusion coverage and accuracy; the Agilent DNA-based assay also showed notable false positives and missed fusions.
Conclusions:
- RNA-based parallel sequencing assays are highly effective for detecting targetable gene fusions.
- These methods are valuable tools for clinical diagnostics in lung cancer management.
