A Cross-Sectional Study of Variant Interpretation and Reporting of NGS Data Using Tertiary Analysis Software: Navify® Mutation Profiler
Abstract Introduction Personalized medicine has revolutionized the clinical management of patients with solid tumors. However, the large volumes of molecular data derived from next-generation sequencing (NGS) and the lack of harmonized bioinformatics pipelines drastically impact the clinical managem...
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Adis, Springer Healthcare
2024-11-01
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| Series: | Oncology and Therapy |
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| Online Access: | https://doi.org/10.1007/s40487-024-00316-0 |
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| author | Francesco Pepe Gianluca Russo Nadia Barraco Marco Bono Angela Listì Luisella Righi Dario de Biase Thais Maloberti Claudia Scimone Lucia Palumbo Danilo Rocco Giuseppina Roscigno Enzo Gallo Simonetta Buglioni Michelina Coco Lucia Anna Muscarella Giancarlo Troncone Umberto Malapelle |
| author_facet | Francesco Pepe Gianluca Russo Nadia Barraco Marco Bono Angela Listì Luisella Righi Dario de Biase Thais Maloberti Claudia Scimone Lucia Palumbo Danilo Rocco Giuseppina Roscigno Enzo Gallo Simonetta Buglioni Michelina Coco Lucia Anna Muscarella Giancarlo Troncone Umberto Malapelle |
| author_sort | Francesco Pepe |
| collection | DOAJ |
| description | Abstract Introduction Personalized medicine has revolutionized the clinical management of patients with solid tumors. However, the large volumes of molecular data derived from next-generation sequencing (NGS) and the lack of harmonized bioinformatics pipelines drastically impact the clinical management of patients with solid tumors. A possible solution to streamline the molecular interpretation and reporting of NGS data would be to adopt automated data analysis software. In this study, we tested the clinical efficiency of the Navify Mutation Profiler (nMP) software in improving the interpretation of NGS data analysis in diagnostic routine samples from patients with solid tumors. Methods This study included one coordinating institution (Federico II University of Naples) and five other Italian institutions. Variant call format (VCF) files from reference standard samples previously tested by the coordinating institution and from n = 8 diagnostic routine samples (n = 2 from colorectal carcinoma; n = 2 from non-small cell lung cancer; n = 2 from advanced melanoma; and n = 2 from patients with gastrointestinal stromal tumors) and previously analyzed by each participating institution (n = 5) with standardized internal analysis workflows were uploaded onto the Navify® Mutation Profiler (nMP) system (Roche Sequencing Solutions, Pleasanton, CA, USA) for automated analysis and interpretation of DNA and RNA molecular alterations analytical parameters, molecular profiling, and clinical interpretation were carried out by the nMP system and compared with the standard workflow data analyzed by the participating institutions. Results Overall, all VCF files were successfully submitted and interpreted by the nMP system. A concordance agreement rate of 89.6% was observed between the automated and standard workflow systems. In particular, DNA and RNA molecular profiles obtained with the nMP system matched those obtained with standardized approaches in 44 out of 48 patients (91.7%) and in 11 out of 12 (91.7%) cases, respectively. In addition, the nMP system evidenced wild-type variants in 6 out of 7 (85.7%) cases. Conclusions The nMP system represents a valid, easily manageable, and clinically useful system to interpret NGS data on diagnostic routine samples from patients with solid tumors. |
| format | Article |
| id | doaj-art-e4dcff2a52fe489397cd1fff0c902ec1 |
| institution | OA Journals |
| issn | 2366-1070 2366-1089 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Adis, Springer Healthcare |
| record_format | Article |
| series | Oncology and Therapy |
| spelling | doaj-art-e4dcff2a52fe489397cd1fff0c902ec12025-08-20T01:57:45ZengAdis, Springer HealthcareOncology and Therapy2366-10702366-10892024-11-0113111513010.1007/s40487-024-00316-0A Cross-Sectional Study of Variant Interpretation and Reporting of NGS Data Using Tertiary Analysis Software: Navify® Mutation ProfilerFrancesco Pepe0Gianluca Russo1Nadia Barraco2Marco Bono3Angela Listì4Luisella Righi5Dario de Biase6Thais Maloberti7Claudia Scimone8Lucia Palumbo9Danilo Rocco10Giuseppina Roscigno11Enzo Gallo12Simonetta Buglioni13Michelina Coco14Lucia Anna Muscarella15Giancarlo Troncone16Umberto Malapelle17Department of Public Health, Federico II University of NaplesDepartment of Public Health, Federico II University of NaplesDepartment of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), University of PalermoDepartment of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), University of PalermoDepartment of Oncology, University of Turin, San Luigi HospitalDepartment of Oncology, University of Turin, San Luigi HospitalDepartment of Pharmacy and Biotechnology (FaBiT), University of BolognaSolid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero—Universitaria di BolognaDepartment of Public Health, Federico II University of NaplesDepartment of Public Health, Federico II University of NaplesDepartment of Pulmonary Oncology, AORN dei Colli MonaldiDepartment of Biology, Federico II University of NaplesDepartment of Pathology, IRCCS Regina Elena National Cancer InstituteDepartment of Pathology, IRCCS Regina Elena National Cancer InstituteLaboratory of Oncology, Fondazione IRCCS Ospedale Casa Sollievo della SofferenzaLaboratory of Oncology, Fondazione IRCCS Ospedale Casa Sollievo della SofferenzaDepartment of Public Health, Federico II University of NaplesDepartment of Public Health, Federico II University of NaplesAbstract Introduction Personalized medicine has revolutionized the clinical management of patients with solid tumors. However, the large volumes of molecular data derived from next-generation sequencing (NGS) and the lack of harmonized bioinformatics pipelines drastically impact the clinical management of patients with solid tumors. A possible solution to streamline the molecular interpretation and reporting of NGS data would be to adopt automated data analysis software. In this study, we tested the clinical efficiency of the Navify Mutation Profiler (nMP) software in improving the interpretation of NGS data analysis in diagnostic routine samples from patients with solid tumors. Methods This study included one coordinating institution (Federico II University of Naples) and five other Italian institutions. Variant call format (VCF) files from reference standard samples previously tested by the coordinating institution and from n = 8 diagnostic routine samples (n = 2 from colorectal carcinoma; n = 2 from non-small cell lung cancer; n = 2 from advanced melanoma; and n = 2 from patients with gastrointestinal stromal tumors) and previously analyzed by each participating institution (n = 5) with standardized internal analysis workflows were uploaded onto the Navify® Mutation Profiler (nMP) system (Roche Sequencing Solutions, Pleasanton, CA, USA) for automated analysis and interpretation of DNA and RNA molecular alterations analytical parameters, molecular profiling, and clinical interpretation were carried out by the nMP system and compared with the standard workflow data analyzed by the participating institutions. Results Overall, all VCF files were successfully submitted and interpreted by the nMP system. A concordance agreement rate of 89.6% was observed between the automated and standard workflow systems. In particular, DNA and RNA molecular profiles obtained with the nMP system matched those obtained with standardized approaches in 44 out of 48 patients (91.7%) and in 11 out of 12 (91.7%) cases, respectively. In addition, the nMP system evidenced wild-type variants in 6 out of 7 (85.7%) cases. Conclusions The nMP system represents a valid, easily manageable, and clinically useful system to interpret NGS data on diagnostic routine samples from patients with solid tumors.https://doi.org/10.1007/s40487-024-00316-0Navify ® Mutation Profiler (nMP)Molecular pathologyTumor biomarkersDiagnostic techniques and procedures |
| spellingShingle | Francesco Pepe Gianluca Russo Nadia Barraco Marco Bono Angela Listì Luisella Righi Dario de Biase Thais Maloberti Claudia Scimone Lucia Palumbo Danilo Rocco Giuseppina Roscigno Enzo Gallo Simonetta Buglioni Michelina Coco Lucia Anna Muscarella Giancarlo Troncone Umberto Malapelle A Cross-Sectional Study of Variant Interpretation and Reporting of NGS Data Using Tertiary Analysis Software: Navify® Mutation Profiler Oncology and Therapy Navify ® Mutation Profiler (nMP) Molecular pathology Tumor biomarkers Diagnostic techniques and procedures |
| title | A Cross-Sectional Study of Variant Interpretation and Reporting of NGS Data Using Tertiary Analysis Software: Navify® Mutation Profiler |
| title_full | A Cross-Sectional Study of Variant Interpretation and Reporting of NGS Data Using Tertiary Analysis Software: Navify® Mutation Profiler |
| title_fullStr | A Cross-Sectional Study of Variant Interpretation and Reporting of NGS Data Using Tertiary Analysis Software: Navify® Mutation Profiler |
| title_full_unstemmed | A Cross-Sectional Study of Variant Interpretation and Reporting of NGS Data Using Tertiary Analysis Software: Navify® Mutation Profiler |
| title_short | A Cross-Sectional Study of Variant Interpretation and Reporting of NGS Data Using Tertiary Analysis Software: Navify® Mutation Profiler |
| title_sort | cross sectional study of variant interpretation and reporting of ngs data using tertiary analysis software navify r mutation profiler |
| topic | Navify ® Mutation Profiler (nMP) Molecular pathology Tumor biomarkers Diagnostic techniques and procedures |
| url | https://doi.org/10.1007/s40487-024-00316-0 |
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