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Design and Validation of a Gene-Targeted, Next-Generation Sequencing Panel for Routine Diagnosis in Gliomas

The updated 2016 World Health Organization (WHO) classification system for gliomas integrates molecular alterations and histology to provide a greater diagnostic and prognostic utility than the previous, histology-based classification. The increasing number of markers that are tested in a correct di...

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Autores principales: D’Haene, Nicky, Meléndez, Bárbara, Blanchard, Oriane, De Nève, Nancy, Lebrun, Laetitia, Van Campenhout, Claude, Salmon, Isabelle
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6627812/
https://www.ncbi.nlm.nih.gov/pubmed/31167453
http://dx.doi.org/10.3390/cancers11060773
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author D’Haene, Nicky
Meléndez, Bárbara
Blanchard, Oriane
De Nève, Nancy
Lebrun, Laetitia
Van Campenhout, Claude
Salmon, Isabelle
author_facet D’Haene, Nicky
Meléndez, Bárbara
Blanchard, Oriane
De Nève, Nancy
Lebrun, Laetitia
Van Campenhout, Claude
Salmon, Isabelle
author_sort D’Haene, Nicky
collection PubMed
description The updated 2016 World Health Organization (WHO) classification system for gliomas integrates molecular alterations and histology to provide a greater diagnostic and prognostic utility than the previous, histology-based classification. The increasing number of markers that are tested in a correct diagnostic procedure makes gene-targeted, next-generation sequencing (NGS) a powerful tool in routine pathology practice. We designed a 14-gene NGS panel specifically aimed at the diagnosis of glioma, which allows simultaneous detection of mutations and copy number variations, including the 1p/19q-codeletion and Epidermal Growth Factor Receptor (EGFR) amplification. To validate this panel, we used reference mutated DNAs, nontumor and non-glioma samples, and 52 glioma samples that were previously characterized. The panel was then prospectively applied to 91 brain lesions. A specificity of 100% and sensitivity of 99.4% was achieved for mutation detection. Orthogonal methods, such as in situ hybridization and immunohistochemical techniques, were used for validation, which showed high concordance. The molecular alterations that were identified allowed diagnosis according to the updated WHO criteria, and helped in the differential diagnosis of difficult cases. This NGS panel is an accurate and sensitive method, which could replace multiple tests for the same sample. Moreover, it is a rapid and cost-effective approach that can be easily implemented in the routine diagnosis of gliomas.
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spelling pubmed-66278122019-07-23 Design and Validation of a Gene-Targeted, Next-Generation Sequencing Panel for Routine Diagnosis in Gliomas D’Haene, Nicky Meléndez, Bárbara Blanchard, Oriane De Nève, Nancy Lebrun, Laetitia Van Campenhout, Claude Salmon, Isabelle Cancers (Basel) Article The updated 2016 World Health Organization (WHO) classification system for gliomas integrates molecular alterations and histology to provide a greater diagnostic and prognostic utility than the previous, histology-based classification. The increasing number of markers that are tested in a correct diagnostic procedure makes gene-targeted, next-generation sequencing (NGS) a powerful tool in routine pathology practice. We designed a 14-gene NGS panel specifically aimed at the diagnosis of glioma, which allows simultaneous detection of mutations and copy number variations, including the 1p/19q-codeletion and Epidermal Growth Factor Receptor (EGFR) amplification. To validate this panel, we used reference mutated DNAs, nontumor and non-glioma samples, and 52 glioma samples that were previously characterized. The panel was then prospectively applied to 91 brain lesions. A specificity of 100% and sensitivity of 99.4% was achieved for mutation detection. Orthogonal methods, such as in situ hybridization and immunohistochemical techniques, were used for validation, which showed high concordance. The molecular alterations that were identified allowed diagnosis according to the updated WHO criteria, and helped in the differential diagnosis of difficult cases. This NGS panel is an accurate and sensitive method, which could replace multiple tests for the same sample. Moreover, it is a rapid and cost-effective approach that can be easily implemented in the routine diagnosis of gliomas. MDPI 2019-06-04 /pmc/articles/PMC6627812/ /pubmed/31167453 http://dx.doi.org/10.3390/cancers11060773 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
D’Haene, Nicky
Meléndez, Bárbara
Blanchard, Oriane
De Nève, Nancy
Lebrun, Laetitia
Van Campenhout, Claude
Salmon, Isabelle
Design and Validation of a Gene-Targeted, Next-Generation Sequencing Panel for Routine Diagnosis in Gliomas
title Design and Validation of a Gene-Targeted, Next-Generation Sequencing Panel for Routine Diagnosis in Gliomas
title_full Design and Validation of a Gene-Targeted, Next-Generation Sequencing Panel for Routine Diagnosis in Gliomas
title_fullStr Design and Validation of a Gene-Targeted, Next-Generation Sequencing Panel for Routine Diagnosis in Gliomas
title_full_unstemmed Design and Validation of a Gene-Targeted, Next-Generation Sequencing Panel for Routine Diagnosis in Gliomas
title_short Design and Validation of a Gene-Targeted, Next-Generation Sequencing Panel for Routine Diagnosis in Gliomas
title_sort design and validation of a gene-targeted, next-generation sequencing panel for routine diagnosis in gliomas
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6627812/
https://www.ncbi.nlm.nih.gov/pubmed/31167453
http://dx.doi.org/10.3390/cancers11060773
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