Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation

Language
en
Document Type
Article
Issue Date
2021-12-01
Issue Year
2021
Authors
Heydt, Carina
Wölwer, Christina B.
Velazquez Camacho, Oscar
Wagener-Ryczek, Svenja
Pappesch, Roberto
Siemanowski, Janna
Rehker, Jan
Haller, Florian
Agaimy, Abbas
Worm, Karl
Editor
Abstract

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.

Journal Title
BMC Medical Genomics
Volume
14
Citation
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