Targeted RNA-sequencing analysis for fusion transcripts detection in tumor diagnostics: assessment of bioinformatic tools reliability in FFPE samples
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 det...
| Main Authors: | , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Open Exploration Publishing Inc.
2022-10-01
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| Series: | Exploration of Targeted Anti-tumor Therapy |
| Subjects: | |
| Online Access: | https://www.explorationpub.com/Journals/etat/Article/1002102 |
| _version_ | 1828731410980012032 |
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| author | Iolanda Capone Fabio Bozzi Gian Paolo Dagrada Paolo Verderio Elena Conca Adele Busico Maria Adele Testi Valentina Monti Matteo Duca Claudia Proto Silvia Damian Alberta Piccolo Federica Perrone Elena Tamborini Andrea Devecchi Paola Collini Daniele Lorenzini Andrea Vingiani Luca Agnelli Giancarlo Pruneri |
| author_facet | Iolanda Capone Fabio Bozzi Gian Paolo Dagrada Paolo Verderio Elena Conca Adele Busico Maria Adele Testi Valentina Monti Matteo Duca Claudia Proto Silvia Damian Alberta Piccolo Federica Perrone Elena Tamborini Andrea Devecchi Paola Collini Daniele Lorenzini Andrea Vingiani Luca Agnelli Giancarlo Pruneri |
| author_sort | Iolanda Capone |
| collection | DOAJ |
| description | 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© 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© 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.
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. |
| first_indexed | 2024-04-12T17:45:39Z |
| format | Article |
| id | doaj.art-d74b17c328cc45588837b22f3835282c |
| institution | Directory Open Access Journal |
| issn | 2692-3114 |
| language | English |
| last_indexed | 2024-04-12T17:45:39Z |
| publishDate | 2022-10-01 |
| publisher | Open Exploration Publishing Inc. |
| record_format | Article |
| series | Exploration of Targeted Anti-tumor Therapy |
| spelling | doaj.art-d74b17c328cc45588837b22f3835282c2022-12-22T03:22:41ZengOpen Exploration Publishing Inc.Exploration of Targeted Anti-tumor Therapy2692-31142022-10-013558259710.37349/etat.2022.00102Targeted RNA-sequencing analysis for fusion transcripts detection in tumor diagnostics: assessment of bioinformatic tools reliability in FFPE samplesIolanda Capone0https://orcid.org/0000-0002-6572-614XFabio Bozzi1https://orcid.org/0000-0003-0729-1288Gian Paolo Dagrada2https://orcid.org/0000-0002-6743-1935Paolo Verderio3https://orcid.org/0000-0002-9231-1281Elena Conca4https://orcid.org/0000-0003-2052-8104Adele Busico5https://orcid.org/0000-0002-5808-0387Maria Adele Testi6https://orcid.org/0000-0002-9462-0336Valentina Monti7https://orcid.org/0000-0003-1459-384XMatteo Duca8https://orcid.org/0000-0003-3968-5011Claudia Proto9https://orcid.org/0000-0003-0287-9787Silvia Damian10https://orcid.org/0000-0001-9560-1092Alberta Piccolo11https://orcid.org/0000-0003-2078-9988Federica Perrone12https://orcid.org/0000-0003-4406-8245Elena Tamborini13https://orcid.org/0000-0002-3819-8687Andrea Devecchi14https://orcid.org/0000-0003-0440-3221Paola Collini15https://orcid.org/0000-0002-6158-210XDaniele Lorenzini16https://orcid.org/0000-0002-1425-3354Andrea Vingiani17https://orcid.org/0000-0002-9827-3976Luca Agnelli18https://orcid.org/0000-0003-0582-6170Giancarlo Pruneri19https://orcid.org/0000-0002-7963-7172Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy; Department of Oncology and Hemato-oncology, University of Milan, 20133 Milan, ItalyDepartment of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy; Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, ItalyDepartment of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy; Department of Oncology and Hemato-oncology, University of Milan, 20133 Milan, ItalyAim: 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© 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© 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. 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.https://www.explorationpub.com/Journals/etat/Article/1002102next-generation sequencing (ngs)rna-sequencingfluorescence in situ hybridization (fish)formalin-fixed paraffin-embedded (ffpe)gene fusions |
| spellingShingle | Iolanda Capone Fabio Bozzi Gian Paolo Dagrada Paolo Verderio Elena Conca Adele Busico Maria Adele Testi Valentina Monti Matteo Duca Claudia Proto Silvia Damian Alberta Piccolo Federica Perrone Elena Tamborini Andrea Devecchi Paola Collini Daniele Lorenzini Andrea Vingiani Luca Agnelli Giancarlo Pruneri Targeted RNA-sequencing analysis for fusion transcripts detection in tumor diagnostics: assessment of bioinformatic tools reliability in FFPE samples Exploration of Targeted Anti-tumor Therapy next-generation sequencing (ngs) rna-sequencing fluorescence in situ hybridization (fish) formalin-fixed paraffin-embedded (ffpe) gene fusions |
| title | Targeted RNA-sequencing analysis for fusion transcripts detection in tumor diagnostics: assessment of bioinformatic tools reliability in FFPE samples |
| title_full | Targeted RNA-sequencing analysis for fusion transcripts detection in tumor diagnostics: assessment of bioinformatic tools reliability in FFPE samples |
| title_fullStr | Targeted RNA-sequencing analysis for fusion transcripts detection in tumor diagnostics: assessment of bioinformatic tools reliability in FFPE samples |
| title_full_unstemmed | Targeted RNA-sequencing analysis for fusion transcripts detection in tumor diagnostics: assessment of bioinformatic tools reliability in FFPE samples |
| title_short | Targeted RNA-sequencing analysis for fusion transcripts detection in tumor diagnostics: assessment of bioinformatic tools reliability in FFPE samples |
| title_sort | targeted rna sequencing analysis for fusion transcripts detection in tumor diagnostics assessment of bioinformatic tools reliability in ffpe samples |
| topic | next-generation sequencing (ngs) rna-sequencing fluorescence in situ hybridization (fish) formalin-fixed paraffin-embedded (ffpe) gene fusions |
| url | https://www.explorationpub.com/Journals/etat/Article/1002102 |
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