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...
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Autor*in:	Carina Heydt [verfasserIn] Christina B. Wölwer [verfasserIn] Oscar Velazquez Camacho [verfasserIn] Svenja Wagener-Ryczek [verfasserIn] Roberto Pappesch [verfasserIn] Janna Siemanowski [verfasserIn] Jan Rehker [verfasserIn] Florian Haller [verfasserIn] Abbas Agaimy [verfasserIn] Karl Worm [verfasserIn] Thomas Herold [verfasserIn] Nicole Pfarr [verfasserIn] Wilko Weichert [verfasserIn] Thomas Kirchner [verfasserIn] Andreas Jung [verfasserIn] Jörg Kumbrink [verfasserIn] Wolfgang Goering [verfasserIn] Irene Esposito [verfasserIn] Reinhard Buettner [verfasserIn] Axel M. Hillmer [verfasserIn] Sabine Merkelbach-Bruse [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2021

Schlagwörter:	NGS FISH Gene fusion DNA-Seq RNA-seq

Übergeordnetes Werk:	In: BMC Medical Genomics - BMC, 2008, 14(2021), 1, Seite 14
Übergeordnetes Werk:	volume:14 ; year:2021 ; number:1 ; pages:14

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/s12920-021-00909-y

Katalog-ID:	DOAJ007043538

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520			\|a 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.
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700	0		\|a Svenja Wagener-Ryczek \|e verfasserin \|4 aut
700	0		\|a Roberto Pappesch \|e verfasserin \|4 aut
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700	0		\|a Wolfgang Goering \|e verfasserin \|4 aut
700	0		\|a Irene Esposito \|e verfasserin \|4 aut
700	0		\|a Reinhard Buettner \|e verfasserin \|4 aut
700	0		\|a Axel M. Hillmer \|e verfasserin \|4 aut
700	0		\|a Sabine Merkelbach-Bruse \|e verfasserin \|4 aut
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allfields	10.1186/s12920-021-00909-y doi (DE-627)DOAJ007043538 (DE-599)DOAJ44bdb1f0d72743ee9374126053306f77 DE-627 ger DE-627 rakwb eng RC31-1245 QH426-470 Carina Heydt verfasserin aut Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. NGS FISH Gene fusion DNA-Seq RNA-seq Internal medicine Genetics Christina B. Wölwer verfasserin aut Oscar Velazquez Camacho verfasserin aut Svenja Wagener-Ryczek verfasserin aut Roberto Pappesch verfasserin aut Janna Siemanowski verfasserin aut Jan Rehker verfasserin aut Florian Haller verfasserin aut Abbas Agaimy verfasserin aut Karl Worm verfasserin aut Thomas Herold verfasserin aut Nicole Pfarr verfasserin aut Wilko Weichert verfasserin aut Thomas Kirchner verfasserin aut Andreas Jung verfasserin aut Jörg Kumbrink verfasserin aut Wolfgang Goering verfasserin aut Irene Esposito verfasserin aut Reinhard Buettner verfasserin aut Axel M. Hillmer verfasserin aut Sabine Merkelbach-Bruse verfasserin aut In BMC Medical Genomics BMC, 2008 14(2021), 1, Seite 14 (DE-627)559080824 (DE-600)2411865-5 17558794 nnns volume:14 year:2021 number:1 pages:14 https://doi.org/10.1186/s12920-021-00909-y kostenfrei https://doaj.org/article/44bdb1f0d72743ee9374126053306f77 kostenfrei https://doi.org/10.1186/s12920-021-00909-y kostenfrei https://doaj.org/toc/1755-8794 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 14 2021 1 14
spelling	10.1186/s12920-021-00909-y doi (DE-627)DOAJ007043538 (DE-599)DOAJ44bdb1f0d72743ee9374126053306f77 DE-627 ger DE-627 rakwb eng RC31-1245 QH426-470 Carina Heydt verfasserin aut Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. NGS FISH Gene fusion DNA-Seq RNA-seq Internal medicine Genetics Christina B. Wölwer verfasserin aut Oscar Velazquez Camacho verfasserin aut Svenja Wagener-Ryczek verfasserin aut Roberto Pappesch verfasserin aut Janna Siemanowski verfasserin aut Jan Rehker verfasserin aut Florian Haller verfasserin aut Abbas Agaimy verfasserin aut Karl Worm verfasserin aut Thomas Herold verfasserin aut Nicole Pfarr verfasserin aut Wilko Weichert verfasserin aut Thomas Kirchner verfasserin aut Andreas Jung verfasserin aut Jörg Kumbrink verfasserin aut Wolfgang Goering verfasserin aut Irene Esposito verfasserin aut Reinhard Buettner verfasserin aut Axel M. Hillmer verfasserin aut Sabine Merkelbach-Bruse verfasserin aut In BMC Medical Genomics BMC, 2008 14(2021), 1, Seite 14 (DE-627)559080824 (DE-600)2411865-5 17558794 nnns volume:14 year:2021 number:1 pages:14 https://doi.org/10.1186/s12920-021-00909-y kostenfrei https://doaj.org/article/44bdb1f0d72743ee9374126053306f77 kostenfrei https://doi.org/10.1186/s12920-021-00909-y kostenfrei https://doaj.org/toc/1755-8794 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 14 2021 1 14
allfields_unstemmed	10.1186/s12920-021-00909-y doi (DE-627)DOAJ007043538 (DE-599)DOAJ44bdb1f0d72743ee9374126053306f77 DE-627 ger DE-627 rakwb eng RC31-1245 QH426-470 Carina Heydt verfasserin aut Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. NGS FISH Gene fusion DNA-Seq RNA-seq Internal medicine Genetics Christina B. Wölwer verfasserin aut Oscar Velazquez Camacho verfasserin aut Svenja Wagener-Ryczek verfasserin aut Roberto Pappesch verfasserin aut Janna Siemanowski verfasserin aut Jan Rehker verfasserin aut Florian Haller verfasserin aut Abbas Agaimy verfasserin aut Karl Worm verfasserin aut Thomas Herold verfasserin aut Nicole Pfarr verfasserin aut Wilko Weichert verfasserin aut Thomas Kirchner verfasserin aut Andreas Jung verfasserin aut Jörg Kumbrink verfasserin aut Wolfgang Goering verfasserin aut Irene Esposito verfasserin aut Reinhard Buettner verfasserin aut Axel M. Hillmer verfasserin aut Sabine Merkelbach-Bruse verfasserin aut In BMC Medical Genomics BMC, 2008 14(2021), 1, Seite 14 (DE-627)559080824 (DE-600)2411865-5 17558794 nnns volume:14 year:2021 number:1 pages:14 https://doi.org/10.1186/s12920-021-00909-y kostenfrei https://doaj.org/article/44bdb1f0d72743ee9374126053306f77 kostenfrei https://doi.org/10.1186/s12920-021-00909-y kostenfrei https://doaj.org/toc/1755-8794 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 14 2021 1 14
allfieldsGer	10.1186/s12920-021-00909-y doi (DE-627)DOAJ007043538 (DE-599)DOAJ44bdb1f0d72743ee9374126053306f77 DE-627 ger DE-627 rakwb eng RC31-1245 QH426-470 Carina Heydt verfasserin aut Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. NGS FISH Gene fusion DNA-Seq RNA-seq Internal medicine Genetics Christina B. Wölwer verfasserin aut Oscar Velazquez Camacho verfasserin aut Svenja Wagener-Ryczek verfasserin aut Roberto Pappesch verfasserin aut Janna Siemanowski verfasserin aut Jan Rehker verfasserin aut Florian Haller verfasserin aut Abbas Agaimy verfasserin aut Karl Worm verfasserin aut Thomas Herold verfasserin aut Nicole Pfarr verfasserin aut Wilko Weichert verfasserin aut Thomas Kirchner verfasserin aut Andreas Jung verfasserin aut Jörg Kumbrink verfasserin aut Wolfgang Goering verfasserin aut Irene Esposito verfasserin aut Reinhard Buettner verfasserin aut Axel M. Hillmer verfasserin aut Sabine Merkelbach-Bruse verfasserin aut In BMC Medical Genomics BMC, 2008 14(2021), 1, Seite 14 (DE-627)559080824 (DE-600)2411865-5 17558794 nnns volume:14 year:2021 number:1 pages:14 https://doi.org/10.1186/s12920-021-00909-y kostenfrei https://doaj.org/article/44bdb1f0d72743ee9374126053306f77 kostenfrei https://doi.org/10.1186/s12920-021-00909-y kostenfrei https://doaj.org/toc/1755-8794 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 14 2021 1 14
allfieldsSound	10.1186/s12920-021-00909-y doi (DE-627)DOAJ007043538 (DE-599)DOAJ44bdb1f0d72743ee9374126053306f77 DE-627 ger DE-627 rakwb eng RC31-1245 QH426-470 Carina Heydt verfasserin aut Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. NGS FISH Gene fusion DNA-Seq RNA-seq Internal medicine Genetics Christina B. Wölwer verfasserin aut Oscar Velazquez Camacho verfasserin aut Svenja Wagener-Ryczek verfasserin aut Roberto Pappesch verfasserin aut Janna Siemanowski verfasserin aut Jan Rehker verfasserin aut Florian Haller verfasserin aut Abbas Agaimy verfasserin aut Karl Worm verfasserin aut Thomas Herold verfasserin aut Nicole Pfarr verfasserin aut Wilko Weichert verfasserin aut Thomas Kirchner verfasserin aut Andreas Jung verfasserin aut Jörg Kumbrink verfasserin aut Wolfgang Goering verfasserin aut Irene Esposito verfasserin aut Reinhard Buettner verfasserin aut Axel M. Hillmer verfasserin aut Sabine Merkelbach-Bruse verfasserin aut In BMC Medical Genomics BMC, 2008 14(2021), 1, Seite 14 (DE-627)559080824 (DE-600)2411865-5 17558794 nnns volume:14 year:2021 number:1 pages:14 https://doi.org/10.1186/s12920-021-00909-y kostenfrei https://doaj.org/article/44bdb1f0d72743ee9374126053306f77 kostenfrei https://doi.org/10.1186/s12920-021-00909-y kostenfrei https://doaj.org/toc/1755-8794 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 14 2021 1 14
language	English
source	In BMC Medical Genomics 14(2021), 1, Seite 14 volume:14 year:2021 number:1 pages:14
sourceStr	In BMC Medical Genomics 14(2021), 1, Seite 14 volume:14 year:2021 number:1 pages:14
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	NGS FISH Gene fusion DNA-Seq RNA-seq Internal medicine Genetics
isfreeaccess_bool	true
container_title	BMC Medical Genomics
authorswithroles_txt_mv	Carina Heydt @@aut@@ Christina B. Wölwer @@aut@@ Oscar Velazquez Camacho @@aut@@ Svenja Wagener-Ryczek @@aut@@ Roberto Pappesch @@aut@@ Janna Siemanowski @@aut@@ Jan Rehker @@aut@@ Florian Haller @@aut@@ Abbas Agaimy @@aut@@ Karl Worm @@aut@@ Thomas Herold @@aut@@ Nicole Pfarr @@aut@@ Wilko Weichert @@aut@@ Thomas Kirchner @@aut@@ Andreas Jung @@aut@@ Jörg Kumbrink @@aut@@ Wolfgang Goering @@aut@@ Irene Esposito @@aut@@ Reinhard Buettner @@aut@@ Axel M. Hillmer @@aut@@ Sabine Merkelbach-Bruse @@aut@@
publishDateDaySort_date	2021-01-01T00:00:00Z
hierarchy_top_id	559080824
id	DOAJ007043538
language_de	englisch
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callnumber-first	R - Medicine
author	Carina Heydt
spellingShingle	Carina Heydt misc RC31-1245 misc QH426-470 misc NGS misc FISH misc Gene fusion misc DNA-Seq misc RNA-seq misc Internal medicine misc Genetics Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation
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topic_title	RC31-1245 QH426-470 Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation NGS FISH Gene fusion DNA-Seq RNA-seq
topic	misc RC31-1245 misc QH426-470 misc NGS misc FISH misc Gene fusion misc DNA-Seq misc RNA-seq misc Internal medicine misc Genetics
topic_unstemmed	misc RC31-1245 misc QH426-470 misc NGS misc FISH misc Gene fusion misc DNA-Seq misc RNA-seq misc Internal medicine misc Genetics
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title	Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation
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title_full	Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation
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author_browse	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
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title_sort	detection of gene fusions using targeted next-generation sequencing: a comparative evaluation
callnumber	RC31-1245
title_auth	Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation
abstract	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.
abstractGer	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.
abstract_unstemmed	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.
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title_short	Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation
url	https://doi.org/10.1186/s12920-021-00909-y https://doaj.org/article/44bdb1f0d72743ee9374126053306f77 https://doaj.org/toc/1755-8794
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author2	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
author2Str	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
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Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation

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