Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation
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 lin...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-02-01
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| Series: | BMC Medical Genomics |
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| Online Access: | https://doi.org/10.1186/s12920-021-00909-y |
| _version_ | 1819168214270083072 |
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| author | Carina Heydt Christina B. Wölwer Oscar Velazquez Camacho Svenja Wagener-Ryczek Roberto Pappesch Janna Siemanowski Jan Rehker Florian Haller Abbas Agaimy Karl Worm Thomas Herold Nicole Pfarr Wilko Weichert Thomas Kirchner Andreas Jung Jörg Kumbrink Wolfgang Goering Irene Esposito Reinhard Buettner Axel M. Hillmer Sabine Merkelbach-Bruse |
| author_facet | Carina Heydt Christina B. Wölwer Oscar Velazquez Camacho Svenja Wagener-Ryczek Roberto Pappesch Janna Siemanowski Jan Rehker Florian Haller Abbas Agaimy Karl Worm Thomas Herold Nicole Pfarr Wilko Weichert Thomas Kirchner Andreas Jung Jörg Kumbrink Wolfgang Goering Irene Esposito Reinhard Buettner Axel M. Hillmer Sabine Merkelbach-Bruse |
| author_sort | Carina Heydt |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-22T19:00:03Z |
| format | Article |
| id | doaj.art-44bdb1f0d72743ee9374126053306f77 |
| institution | Directory Open Access Journal |
| issn | 1755-8794 |
| language | English |
| last_indexed | 2024-12-22T19:00:03Z |
| publishDate | 2021-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Genomics |
| spelling | doaj.art-44bdb1f0d72743ee9374126053306f772022-12-21T18:15:58ZengBMCBMC Medical Genomics1755-87942021-02-0114111410.1186/s12920-021-00909-yDetection of gene fusions using targeted next-generation sequencing: a comparative evaluationCarina Heydt0Christina B. Wölwer1Oscar Velazquez Camacho2Svenja Wagener-Ryczek3Roberto Pappesch4Janna Siemanowski5Jan Rehker6Florian Haller7Abbas Agaimy8Karl Worm9Thomas Herold10Nicole Pfarr11Wilko Weichert12Thomas Kirchner13Andreas Jung14Jörg Kumbrink15Wolfgang Goering16Irene Esposito17Reinhard Buettner18Axel M. Hillmer19Sabine Merkelbach-Bruse20Institute of Pathology, University Hospital CologneInstitute of Pathology, University Hospital CologneInstitute of Pathology, University Hospital CologneInstitute of Pathology, University Hospital CologneInstitute of Pathology, University Hospital CologneInstitute of Pathology, University Hospital CologneInstitute of Pathology, University Hospital CologneInstitute of Pathology, University Hospital ErlangenInstitute of Pathology, University Hospital ErlangenInstitute of Pathology, University Hospital Essen, University Duisburg-EssenInstitute of Pathology, University Hospital Essen, University Duisburg-EssenInstitute of Pathology, Technical University Munich (TUM)Institute of Pathology, Technical University Munich (TUM)Institute of Pathology, LMU MunichInstitute of Pathology, LMU MunichInstitute of Pathology, LMU MunichInstitute of Pathology, Medical Faculty, Heinrich-Heine-University and University Hospital DuesseldorfInstitute of Pathology, Medical Faculty, Heinrich-Heine-University and University Hospital DuesseldorfInstitute of Pathology, University Hospital CologneInstitute of Pathology, University Hospital CologneInstitute of Pathology, University Hospital CologneAbstract 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.https://doi.org/10.1186/s12920-021-00909-yNGSFISHGene fusionDNA-SeqRNA-seq |
| spellingShingle | Carina Heydt Christina B. Wölwer Oscar Velazquez Camacho Svenja Wagener-Ryczek Roberto Pappesch Janna Siemanowski Jan Rehker Florian Haller Abbas Agaimy Karl Worm Thomas Herold Nicole Pfarr Wilko Weichert Thomas Kirchner Andreas Jung Jörg Kumbrink Wolfgang Goering Irene Esposito Reinhard Buettner Axel M. Hillmer Sabine Merkelbach-Bruse Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation BMC Medical Genomics NGS FISH Gene fusion DNA-Seq RNA-seq |
| title | Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation |
| title_full | Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation |
| title_fullStr | Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation |
| title_full_unstemmed | Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation |
| title_short | Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation |
| title_sort | detection of gene fusions using targeted next generation sequencing a comparative evaluation |
| topic | NGS FISH Gene fusion DNA-Seq RNA-seq |
| url | https://doi.org/10.1186/s12920-021-00909-y |
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