European Real-World Assessment of the Clinical Validity of a CE-IVD Panel for Ultra-Fast Next-Generation Sequencing in Solid Tumors
Molecular profiling of solid tumors facilitates personalized, targeted therapeutic interventions. The ability to perform next-generation sequencing (NGS), especially from small tissue samples, in a short turnaround time (TAT) is essential to providing results that enable rapid clinical decisions. Th...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-09-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/18/13788 |
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| author | Nicola Normanno José Carlos Machado Edoardo Pescarmona Simonetta Buglioni Lara Navarro Riziero Esposito Abate Anabela Ferro Rob Mensink Matilde Lambiase Virginie Lespinet-Fabre Byron Calgua Philip M. Jermann Marius Ilié Paul Hofman |
| author_facet | Nicola Normanno José Carlos Machado Edoardo Pescarmona Simonetta Buglioni Lara Navarro Riziero Esposito Abate Anabela Ferro Rob Mensink Matilde Lambiase Virginie Lespinet-Fabre Byron Calgua Philip M. Jermann Marius Ilié Paul Hofman |
| author_sort | Nicola Normanno |
| collection | DOAJ |
| description | Molecular profiling of solid tumors facilitates personalized, targeted therapeutic interventions. The ability to perform next-generation sequencing (NGS), especially from small tissue samples, in a short turnaround time (TAT) is essential to providing results that enable rapid clinical decisions. This multicenter study evaluated the performance of a CE in vitro diagnostic (IVD) assay, the Oncomine Dx Express Test, on the Ion Torrent Genexus System for detecting DNA and RNA variants in solid tumors. Eighty-two archived formalin-fixed paraffin embedded (FFPE) tissue samples from lung, colorectal, central nervous system, melanoma, breast, gastric, thyroid, and soft tissue cancers were used to assess the presence of single nucleotide variants (SNVs), insertions and deletions (indels), copy number variations (CNVs), gene fusions, and splice variants. These clinical samples were previously characterized at the various academic centers using orthogonal methods. The Oncomine Dx Express Test showed high performance with 100% concordance with previous characterization for SNVs, indels, CNVs, gene fusions, and splice variants. SNVs and indels with allele frequencies as low as 5% were correctly identified. The test detected all the expected <i>ALK</i>, <i>RET</i>, <i>NTRK1</i>, and <i>ROS1</i> fusion isoforms and <i>MET</i> exon 14-skipping splice variants. The average TAT from extracted nucleic acids to the final variant report was 18.3 h. The Oncomine Dx Express Test in combination with the Ion Torrent Genexus System is a CE-IVD-compliant, performant, and multicenter reproducible method for NGS detection of actionable biomarkers from a range of tumor samples, providing results in a short TAT that could support timely decision- making for targeted therapeutic interventions. |
| first_indexed | 2024-03-10T22:41:30Z |
| format | Article |
| id | doaj.art-bc24236e37804dfa972096fa4a32c729 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T22:41:30Z |
| publishDate | 2023-09-01 |
| publisher | MDPI AG |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-bc24236e37804dfa972096fa4a32c7292023-11-19T11:03:09ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-09-0124181378810.3390/ijms241813788European Real-World Assessment of the Clinical Validity of a CE-IVD Panel for Ultra-Fast Next-Generation Sequencing in Solid TumorsNicola Normanno0José Carlos Machado1Edoardo Pescarmona2Simonetta Buglioni3Lara Navarro4Riziero Esposito Abate5Anabela Ferro6Rob Mensink7Matilde Lambiase8Virginie Lespinet-Fabre9Byron Calgua10Philip M. Jermann11Marius Ilié12Paul Hofman13Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, ItalyInstituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, PortugalI.R.C.C.S. Regina Elena National Cancer Institute, 00144 Rome, ItalyI.R.C.C.S. Regina Elena National Cancer Institute, 00144 Rome, ItalyConsorcio Hospital General de Valencia, 46014 Valencia, SpainCell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, ItalyInstituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, PortugalInstituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, PortugalCell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, ItalyLaboratory of Clinical and Experimental Pathology, Biobank BB-0033-00025, FHU OncoAge, IHU RespirERA, CHU de Nice, Université Côte d’Azur, 06000 Nice, FranceInstitute of Pathology, University Hospital Basel, 4031 Basel, SwitzerlandInstitute of Pathology, University Hospital Basel, 4031 Basel, SwitzerlandLaboratory of Clinical and Experimental Pathology, Biobank BB-0033-00025, FHU OncoAge, IHU RespirERA, CHU de Nice, Université Côte d’Azur, 06000 Nice, FranceLaboratory of Clinical and Experimental Pathology, Biobank BB-0033-00025, FHU OncoAge, IHU RespirERA, CHU de Nice, Université Côte d’Azur, 06000 Nice, FranceMolecular profiling of solid tumors facilitates personalized, targeted therapeutic interventions. The ability to perform next-generation sequencing (NGS), especially from small tissue samples, in a short turnaround time (TAT) is essential to providing results that enable rapid clinical decisions. This multicenter study evaluated the performance of a CE in vitro diagnostic (IVD) assay, the Oncomine Dx Express Test, on the Ion Torrent Genexus System for detecting DNA and RNA variants in solid tumors. Eighty-two archived formalin-fixed paraffin embedded (FFPE) tissue samples from lung, colorectal, central nervous system, melanoma, breast, gastric, thyroid, and soft tissue cancers were used to assess the presence of single nucleotide variants (SNVs), insertions and deletions (indels), copy number variations (CNVs), gene fusions, and splice variants. These clinical samples were previously characterized at the various academic centers using orthogonal methods. The Oncomine Dx Express Test showed high performance with 100% concordance with previous characterization for SNVs, indels, CNVs, gene fusions, and splice variants. SNVs and indels with allele frequencies as low as 5% were correctly identified. The test detected all the expected <i>ALK</i>, <i>RET</i>, <i>NTRK1</i>, and <i>ROS1</i> fusion isoforms and <i>MET</i> exon 14-skipping splice variants. The average TAT from extracted nucleic acids to the final variant report was 18.3 h. The Oncomine Dx Express Test in combination with the Ion Torrent Genexus System is a CE-IVD-compliant, performant, and multicenter reproducible method for NGS detection of actionable biomarkers from a range of tumor samples, providing results in a short TAT that could support timely decision- making for targeted therapeutic interventions.https://www.mdpi.com/1422-0067/24/18/13788CE-IVDnext-generation sequencingbiomarkersmolecular profilingOncomine Dx Express Test |
| spellingShingle | Nicola Normanno José Carlos Machado Edoardo Pescarmona Simonetta Buglioni Lara Navarro Riziero Esposito Abate Anabela Ferro Rob Mensink Matilde Lambiase Virginie Lespinet-Fabre Byron Calgua Philip M. Jermann Marius Ilié Paul Hofman European Real-World Assessment of the Clinical Validity of a CE-IVD Panel for Ultra-Fast Next-Generation Sequencing in Solid Tumors International Journal of Molecular Sciences CE-IVD next-generation sequencing biomarkers molecular profiling Oncomine Dx Express Test |
| title | European Real-World Assessment of the Clinical Validity of a CE-IVD Panel for Ultra-Fast Next-Generation Sequencing in Solid Tumors |
| title_full | European Real-World Assessment of the Clinical Validity of a CE-IVD Panel for Ultra-Fast Next-Generation Sequencing in Solid Tumors |
| title_fullStr | European Real-World Assessment of the Clinical Validity of a CE-IVD Panel for Ultra-Fast Next-Generation Sequencing in Solid Tumors |
| title_full_unstemmed | European Real-World Assessment of the Clinical Validity of a CE-IVD Panel for Ultra-Fast Next-Generation Sequencing in Solid Tumors |
| title_short | European Real-World Assessment of the Clinical Validity of a CE-IVD Panel for Ultra-Fast Next-Generation Sequencing in Solid Tumors |
| title_sort | european real world assessment of the clinical validity of a ce ivd panel for ultra fast next generation sequencing in solid tumors |
| topic | CE-IVD next-generation sequencing biomarkers molecular profiling Oncomine Dx Express Test |
| url | https://www.mdpi.com/1422-0067/24/18/13788 |
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