PMID- 36338518
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20221108
IS  - 2692-3114 (Electronic)
IS  - 2692-3114 (Linking)
VI  - 3
IP  - 5
DP  - 2022
TI  - Targeted RNA-sequencing analysis for fusion transcripts detection in tumor 
      diagnostics: assessment of bioinformatic tools reliability in FFPE samples.
PG  - 582-597
LID - 10.37349/etat.2022.00102 [doi]
AB  - AIM: 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. The present study is aimed at assessing the overall accuracy of 
      RNA fusion transcripts detection by NGS analysis in FFPE samples in real-world 
      diagnostics. METHODS: 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((c)) 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)]. RESULTS: The combination of FusionPlex((c)) Solid tumor with ArcherDX((R)) 
      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. CONCLUSIONS: 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.
CI  - (c) The Author(s) 2022.
FAU - Capone, Iolanda
AU  - Capone I
AUID- ORCID: 0000-0002-6572-614X
AD  - Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto 
      Nazionale dei Tumori, 20133 Milan, Italy.
FAU - Bozzi, Fabio
AU  - Bozzi F
AUID- ORCID: 0000-0003-0729-1288
AD  - Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto 
      Nazionale dei Tumori, 20133 Milan, Italy.
FAU - Dagrada, Gian Paolo
AU  - Dagrada GP
AUID- ORCID: 0000-0002-6743-1935
AD  - Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto 
      Nazionale dei Tumori, 20133 Milan, Italy.
FAU - Verderio, Paolo
AU  - Verderio P
AUID- ORCID: 0000-0002-9231-1281
AD  - Department of Applied Research and Technological Development, Fondazione IRCCS 
      Istituto Nazionale dei Tumori, 20133 Milan, Italy.
FAU - Conca, Elena
AU  - Conca E
AUID- ORCID: 0000-0003-2052-8104
AD  - Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto 
      Nazionale dei Tumori, 20133 Milan, Italy.
FAU - Busico, Adele
AU  - Busico A
AUID- ORCID: 0000-0002-5808-0387
AD  - Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto 
      Nazionale dei Tumori, 20133 Milan, Italy.
FAU - Testi, Maria Adele
AU  - Testi MA
AUID- ORCID: 0000-0002-9462-0336
AD  - Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto 
      Nazionale dei Tumori, 20133 Milan, Italy.
FAU - Monti, Valentina
AU  - Monti V
AUID- ORCID: 0000-0003-1459-384X
AD  - Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto 
      Nazionale dei Tumori, 20133 Milan, Italy.
FAU - Duca, Matteo
AU  - Duca M
AUID- ORCID: 0000-0003-3968-5011
AD  - Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 
      20133 Milan, Italy.
FAU - Proto, Claudia
AU  - Proto C
AUID- ORCID: 0000-0003-0287-9787
AD  - Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 
      20133 Milan, Italy.
FAU - Damian, Silvia
AU  - Damian S
AUID- ORCID: 0000-0001-9560-1092
AD  - Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 
      20133 Milan, Italy.
FAU - Piccolo, Alberta
AU  - Piccolo A
AUID- ORCID: 0000-0003-2078-9988
AD  - Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto 
      Nazionale dei Tumori, 20133 Milan, Italy.
FAU - Perrone, Federica
AU  - Perrone F
AUID- ORCID: 0000-0003-4406-8245
AD  - Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto 
      Nazionale dei Tumori, 20133 Milan, Italy.
FAU - Tamborini, Elena
AU  - Tamborini E
AUID- ORCID: 0000-0002-3819-8687
AD  - Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto 
      Nazionale dei Tumori, 20133 Milan, Italy.
FAU - Devecchi, Andrea
AU  - Devecchi A
AUID- ORCID: 0000-0003-0440-3221
AD  - Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto 
      Nazionale dei Tumori, 20133 Milan, Italy.
FAU - Collini, Paola
AU  - Collini P
AUID- ORCID: 0000-0002-6158-210X
AD  - Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto 
      Nazionale dei Tumori, 20133 Milan, Italy.
FAU - Lorenzini, Daniele
AU  - Lorenzini D
AUID- ORCID: 0000-0002-1425-3354
AD  - Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto 
      Nazionale dei Tumori, 20133 Milan, Italy.
FAU - Vingiani, Andrea
AU  - Vingiani A
AUID- ORCID: 0000-0002-9827-3976
AD  - Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto 
      Nazionale dei Tumori, 20133 Milan, Italy.
AD  - Department of Oncology and Hemato-oncology, University of Milan, 20133 Milan, 
      Italy.
FAU - Agnelli, Luca
AU  - Agnelli L
AUID- ORCID: 0000-0003-0582-6170
AD  - Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto 
      Nazionale dei Tumori, 20133 Milan, Italy.
AD  - Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 
      20133 Milan, Italy.
FAU - Pruneri, Giancarlo
AU  - Pruneri G
AUID- ORCID: 0000-0002-7963-7172
AD  - Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto 
      Nazionale dei Tumori, 20133 Milan, Italy.
AD  - Department of Oncology and Hemato-oncology, University of Milan, 20133 Milan, 
      Italy.
LA  - eng
PT  - Journal Article
DEP - 20221027
PL  - United States
TA  - Explor Target Antitumor Ther
JT  - Exploration of targeted anti-tumor therapy
JID - 101770662
PMC - PMC9630092
OTO - NOTNLM
OT  - Next-generation sequencing (NGS)
OT  - RNA-sequencing
OT  - fluorescence in situ hybridization (FISH)
OT  - formalin-fixed paraffin-embedded (FFPE)
OT  - gene fusions
COIS- The authors declare that they have no conflicts of interest.
EDAT- 2022/11/08 06:00
MHDA- 2022/11/08 06:01
PMCR- 2022/10/27
CRDT- 2022/11/07 04:29
PHST- 2022/04/29 00:00 [received]
PHST- 2022/08/02 00:00 [accepted]
PHST- 2022/11/07 04:29 [entrez]
PHST- 2022/11/08 06:00 [pubmed]
PHST- 2022/11/08 06:01 [medline]
PHST- 2022/10/27 00:00 [pmc-release]
AID - etat-03-1002102 [pii]
AID - 10.37349/etat.2022.00102 [doi]
PST - ppublish
SO  - Explor Target Antitumor Ther. 2022;3(5):582-597. doi: 10.37349/etat.2022.00102. 
      Epub 2022 Oct 27.