Universität zu Köln

Heydt, Carina, Woelwer, Christina B., Camacho, Oscar Velazquez, Wagener-Ryczek, Svenja, Pappesch, Roberto, Siemanowski, Janna, Rehker, Jan, Haller, Florian, Agaimy, Abbas, Worm, Karl, Herold, Thomas, Pfarr, Nicole, Weichert, Wilko, Kirchner, Thomas, Jung, Andreas, Kumbrink, Joerg, Goering, Wolfgang, Esposito, Irene, Buettner, Reinhard, Hillmer, Axel M. and Merkelbach-Bruse, Sabine (2021). Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation. BMC Med. Genomics, 14 (1). LONDON: BMC. ISSN 1755-8794

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Abstract

BackgroundGene fusions represent promising targets for cancer therapy in lung cancer. Reliable detection of multiple gene fusions is therefore essential. MethodsFive 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).ResultsThe 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.ConclusionsIn summary, especially RNA-based parallel sequencing approaches are potent tools for reliable detection of targetable gene fusions in clinical diagnostics.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Heydt, Carina UNSPECIFIED UNSPECIFIED UNSPECIFIED Woelwer, Christina B. UNSPECIFIED UNSPECIFIED UNSPECIFIED Camacho, Oscar Velazquez UNSPECIFIED UNSPECIFIED UNSPECIFIED Wagener-Ryczek, Svenja UNSPECIFIED UNSPECIFIED UNSPECIFIED Pappesch, Roberto UNSPECIFIED UNSPECIFIED UNSPECIFIED Siemanowski, Janna UNSPECIFIED UNSPECIFIED UNSPECIFIED Rehker, Jan UNSPECIFIED UNSPECIFIED UNSPECIFIED Haller, Florian UNSPECIFIED UNSPECIFIED UNSPECIFIED Agaimy, Abbas UNSPECIFIED UNSPECIFIED UNSPECIFIED Worm, Karl UNSPECIFIED UNSPECIFIED UNSPECIFIED Herold, Thomas UNSPECIFIED UNSPECIFIED UNSPECIFIED Pfarr, Nicole UNSPECIFIED UNSPECIFIED UNSPECIFIED Weichert, Wilko UNSPECIFIED UNSPECIFIED UNSPECIFIED Kirchner, Thomas UNSPECIFIED UNSPECIFIED UNSPECIFIED Jung, Andreas UNSPECIFIED UNSPECIFIED UNSPECIFIED Kumbrink, Joerg UNSPECIFIED UNSPECIFIED UNSPECIFIED Goering, Wolfgang UNSPECIFIED UNSPECIFIED UNSPECIFIED Esposito, Irene UNSPECIFIED UNSPECIFIED UNSPECIFIED Buettner, Reinhard UNSPECIFIED UNSPECIFIED UNSPECIFIED Hillmer, Axel M. UNSPECIFIED UNSPECIFIED UNSPECIFIED Merkelbach-Bruse, Sabine UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-594992
DOI:	10.1186/s12920-021-00909-y
Journal or Publication Title:	BMC Med. Genomics
Volume:	14
Number:	1
Date:	2021
Publisher:	BMC
Place of Publication:	LONDON
ISSN:	1755-8794
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language Genetics & Heredity Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/59499