@article{10.37349/etat.2022.00102,
abstract = {Diagnostic laboratories are progressively introducing next-generation sequencing (NGS) technologies in the routine workflow to meet the increasing clinical need for comprehensive molecular characterization in cancer patients for diagnosis and precision medicine, including fusion-transcripts detection. Nevertheless, the low quality of messenger RNA (mRNA) extracted from formalin-fixed paraffin-embedded (FFPE) samples may affect the transition from traditional single-gene testing approaches [like fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), or polymerase chain reaction (PCR)] to NGS. Herein, NGS data from 190 soft tissue tumors (STTs) and carcinoma cases, discussed in the context of the institutional Molecular Tumor Board, are reported and analyzed by FusionPlex© Solid tumor kit through the manufacturer’s pipeline and by two well-known fast and accurate open-source tools [Arriba (ARR) and spliced transcripts alignment to reference (STAR)-fusion (SFU)]. The combination of FusionPlex© Solid tumor with ArcherDX® Analysis suite (ADx) analysis package has been proven to be sensitive and specific in STT samples, while partial loss of sensitivity has been found in carcinoma specimens. Albeit ARR and SFU showed lower sensitivity, the use of additional fusion-detection tools can contribute to reinforcing or extending the output obtained by ADx, particularly in the case of low-quality input data. Overall, our results sustain the clinical use of NGS for the detection of fusion transcripts in FFPE material.},
author = {Capone, Iolanda and Bozzi, Fabio and Dagrada, Gian Paolo and Verderio, Paolo and Conca, Elena and Busico, Adele and Testi, Maria Adele and Monti, Valentina and Duca, Matteo and Proto, Claudia and Damian, Silvia and Piccolo, Alberta and Perrone, Federica and Tamborini, Elena and Devecchi, Andrea and Collini, Paola and Lorenzini, Daniele and Vingiani, Andrea and Agnelli, Luca and Pruneri, Giancarlo},
doi = {10.37349/etat.2022.00102},
journal = {Exploration of Targeted Anti-tumor Therapy},
pages = {582--597},
title = {{Targeted RNA-sequencing analysis for fusion transcripts detection in tumor diagnostics: assessment of bioinformatic tools reliability in FFPE samples}},
url = {https://www.explorationpub.com/Journals/etat/Article/1002102},
volume = {3},
year = {2022},
number = {5}
}