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Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
Published on: July 5, 2019
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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.
BMC Medical Genomics
|February 28, 2021
Summary
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.
