A Targeted Next-Generation Sequencing Panel to Genotype Gliomas
Gliomas account for the majority of primary brain tumors. Glioblastoma is the most common and malignant type. Based on their extreme molecular heterogeneity, molecular markers can be used to classify gliomas and stratify patients into diagnostic, prognostic, and therapeutic clusters. In this work, w...
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MDPI AG
2022-06-01
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| Online Access: | https://www.mdpi.com/2075-1729/12/7/956 |
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| author | Maria Guarnaccia Laura Guarnaccia Valentina La Cognata Stefania Elena Navone Rolando Campanella Antonella Ampollini Marco Locatelli Monica Miozzo Giovanni Marfia Sebastiano Cavallaro |
| author_facet | Maria Guarnaccia Laura Guarnaccia Valentina La Cognata Stefania Elena Navone Rolando Campanella Antonella Ampollini Marco Locatelli Monica Miozzo Giovanni Marfia Sebastiano Cavallaro |
| author_sort | Maria Guarnaccia |
| collection | DOAJ |
| description | Gliomas account for the majority of primary brain tumors. Glioblastoma is the most common and malignant type. Based on their extreme molecular heterogeneity, molecular markers can be used to classify gliomas and stratify patients into diagnostic, prognostic, and therapeutic clusters. In this work, we developed and validated a targeted next-generation sequencing (NGS) approach to analyze variants or chromosomal aberrations correlated with tumorigenesis and response to treatment in gliomas. Our targeted NGS analysis covered 13 glioma-related genes (<i>ACVR1</i>, <i>ATRX</i>, <i>BRAF</i>, <i>CDKN2A</i>, <i>EGFR</i>, <i>H3F3A</i>, <i>HIST1H3B</i>, <i>HIST1H3C</i>, <i>IDH1</i>, <i>IDH2</i>, <i>P53</i>, <i>PDGFRA</i>, <i>PTEN</i>), a 125 bp region of the <i>TERT</i> promoter, and 54 single nucleotide polymorphisms (SNPs) along chromosomes 1 and 19 for reliable assessment of their copy number alterations (CNAs). Our targeted NGS approach provided a portrait of gliomas’ molecular heterogeneity with high accuracy, specificity, and sensitivity in a single workflow, enabling the detection of variants associated with unfavorable outcomes, disease progression, and drug resistance. These preliminary results support its use in routine diagnostic neuropathology. |
| first_indexed | 2024-03-09T10:16:08Z |
| format | Article |
| id | doaj.art-2264e534f03d40d390657aad452b194f |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-09T10:16:08Z |
| publishDate | 2022-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-2264e534f03d40d390657aad452b194f2023-12-01T22:21:39ZengMDPI AGLife2075-17292022-06-0112795610.3390/life12070956A Targeted Next-Generation Sequencing Panel to Genotype GliomasMaria Guarnaccia0Laura Guarnaccia1Valentina La Cognata2Stefania Elena Navone3Rolando Campanella4Antonella Ampollini5Marco Locatelli6Monica Miozzo7Giovanni Marfia8Sebastiano Cavallaro9Institute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, ItalyLaboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, ItalyInstitute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, ItalyLaboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, ItalyLaboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, ItalyLaboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, ItalyLaboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, ItalyDepartment of Health Sciences, University of Milan, 20122 Milan, ItalyLaboratory of Experimental Neurosurgery and Cell Therapy, Neurosurgery Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, ItalyInstitute for Biomedical Research and Innovation, National Research Council, Via P. Gaifami 18, 95126 Catania, ItalyGliomas account for the majority of primary brain tumors. Glioblastoma is the most common and malignant type. Based on their extreme molecular heterogeneity, molecular markers can be used to classify gliomas and stratify patients into diagnostic, prognostic, and therapeutic clusters. In this work, we developed and validated a targeted next-generation sequencing (NGS) approach to analyze variants or chromosomal aberrations correlated with tumorigenesis and response to treatment in gliomas. Our targeted NGS analysis covered 13 glioma-related genes (<i>ACVR1</i>, <i>ATRX</i>, <i>BRAF</i>, <i>CDKN2A</i>, <i>EGFR</i>, <i>H3F3A</i>, <i>HIST1H3B</i>, <i>HIST1H3C</i>, <i>IDH1</i>, <i>IDH2</i>, <i>P53</i>, <i>PDGFRA</i>, <i>PTEN</i>), a 125 bp region of the <i>TERT</i> promoter, and 54 single nucleotide polymorphisms (SNPs) along chromosomes 1 and 19 for reliable assessment of their copy number alterations (CNAs). Our targeted NGS approach provided a portrait of gliomas’ molecular heterogeneity with high accuracy, specificity, and sensitivity in a single workflow, enabling the detection of variants associated with unfavorable outcomes, disease progression, and drug resistance. These preliminary results support its use in routine diagnostic neuropathology.https://www.mdpi.com/2075-1729/12/7/956glioblastomagliomatargeted sequencingprecision medicinegenomics |
| spellingShingle | Maria Guarnaccia Laura Guarnaccia Valentina La Cognata Stefania Elena Navone Rolando Campanella Antonella Ampollini Marco Locatelli Monica Miozzo Giovanni Marfia Sebastiano Cavallaro A Targeted Next-Generation Sequencing Panel to Genotype Gliomas Life glioblastoma glioma targeted sequencing precision medicine genomics |
| title | A Targeted Next-Generation Sequencing Panel to Genotype Gliomas |
| title_full | A Targeted Next-Generation Sequencing Panel to Genotype Gliomas |
| title_fullStr | A Targeted Next-Generation Sequencing Panel to Genotype Gliomas |
| title_full_unstemmed | A Targeted Next-Generation Sequencing Panel to Genotype Gliomas |
| title_short | A Targeted Next-Generation Sequencing Panel to Genotype Gliomas |
| title_sort | targeted next generation sequencing panel to genotype gliomas |
| topic | glioblastoma glioma targeted sequencing precision medicine genomics |
| url | https://www.mdpi.com/2075-1729/12/7/956 |
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