Comprehensive ngs panel validation for the identification of actionable alterations in adult solid tumors

The increasing identification of driver oncogenic alterations and progress of targeted therapies addresses the need of comprehensive alternatives to standard molecular methods. The translation into clinical practice of next-generation sequencing (NGS) panels is actually challenged by the compliance...

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Autores: Martínez-Fernández, Paula, Pose, Patricia, Dolz-Gaitón, Raquel, García, Arantxa, Trigo-Sánchez, Inmaculada, Rodríguez-Zarco, Enrique, Ríos Martín, Juan José
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2021
País:España
Institución:Universidad de Sevilla (US)
Repositorio:idUS. Depósito de Investigación de la Universidad de Sevilla
OAI Identifier:oai:idus.us.es:11441/116128
Acceso en línea:https://hdl.handle.net/11441/116128
https://doi.org/10.3390/jpm11050360
Access Level:acceso abierto
Palabra clave:Next-generation sequencing (NGS)
Validation
Gene panels
Actionable mutations
Precision oncology
Targeted therapies
Adult solid tumors
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spelling Comprehensive ngs panel validation for the identification of actionable alterations in adult solid tumorsMartínez-Fernández, PaulaPose, PatriciaDolz-Gaitón, RaquelGarcía, ArantxaTrigo-Sánchez, InmaculadaRodríguez-Zarco, EnriqueRíos Martín, Juan JoséNext-generation sequencing (NGS)ValidationGene panelsActionable mutationsPrecision oncologyTargeted therapiesAdult solid tumorsThe increasing identification of driver oncogenic alterations and progress of targeted therapies addresses the need of comprehensive alternatives to standard molecular methods. The translation into clinical practice of next-generation sequencing (NGS) panels is actually challenged by the compliance of high quality standards for clinical accreditation. Herein, we present the analytical and clinical feasibility study of a hybridization capture-based NGS panel (Action OncoKitDx) for the analysis of somatic mutations, copy number variants (CNVs), fusions, pharmacogenetic SNPs and Microsatellite Instability (MSI) determination in formalin-fixed paraffin-embedded (FFPE) tumor samples. A total of 64 samples were submitted to extensive analytical validation for the identification of previously known variants. An additional set of 166 tumor and patient-matched normal samples were sequenced to assess the clinical utility of the assay across different tumor types. The panel demonstrated good specificity, sensitivity, reproducibility, and repeatability for the identification of all biomarkers analyzed and the 5% limit of detection set was validated. Among the clinical cohorts, the assay revealed pathogenic genomic alterations in 97% of patient cases, and in 82.7%, at least one clinically relevant variant was detected. The validation of accuracy and robustness of this assay supports the Action OncoKitDx’s utility in adult solid tumors.MDPICitología e Histología Normal y Patológica2021info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttps://hdl.handle.net/11441/116128https://doi.org/10.3390/jpm11050360reponame:idUS. Depósito de Investigación de la Universidad de Sevillainstname:Universidad de Sevilla (US)InglésJournal of personalized medicine, 11 (5)https://www.mdpi.com/journal/jpminfo:eu-repo/semantics/openAccessoai:idus.us.es:11441/1161282026-06-17T12:51:07Z
dc.title.none.fl_str_mv Comprehensive ngs panel validation for the identification of actionable alterations in adult solid tumors
title Comprehensive ngs panel validation for the identification of actionable alterations in adult solid tumors
spellingShingle Comprehensive ngs panel validation for the identification of actionable alterations in adult solid tumors
Martínez-Fernández, Paula
Next-generation sequencing (NGS)
Validation
Gene panels
Actionable mutations
Precision oncology
Targeted therapies
Adult solid tumors
title_short Comprehensive ngs panel validation for the identification of actionable alterations in adult solid tumors
title_full Comprehensive ngs panel validation for the identification of actionable alterations in adult solid tumors
title_fullStr Comprehensive ngs panel validation for the identification of actionable alterations in adult solid tumors
title_full_unstemmed Comprehensive ngs panel validation for the identification of actionable alterations in adult solid tumors
title_sort Comprehensive ngs panel validation for the identification of actionable alterations in adult solid tumors
dc.creator.none.fl_str_mv Martínez-Fernández, Paula
Pose, Patricia
Dolz-Gaitón, Raquel
García, Arantxa
Trigo-Sánchez, Inmaculada
Rodríguez-Zarco, Enrique
Ríos Martín, Juan José
author Martínez-Fernández, Paula
author_facet Martínez-Fernández, Paula
Pose, Patricia
Dolz-Gaitón, Raquel
García, Arantxa
Trigo-Sánchez, Inmaculada
Rodríguez-Zarco, Enrique
Ríos Martín, Juan José
author_role author
author2 Pose, Patricia
Dolz-Gaitón, Raquel
García, Arantxa
Trigo-Sánchez, Inmaculada
Rodríguez-Zarco, Enrique
Ríos Martín, Juan José
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Citología e Histología Normal y Patológica
dc.subject.none.fl_str_mv Next-generation sequencing (NGS)
Validation
Gene panels
Actionable mutations
Precision oncology
Targeted therapies
Adult solid tumors
topic Next-generation sequencing (NGS)
Validation
Gene panels
Actionable mutations
Precision oncology
Targeted therapies
Adult solid tumors
description The increasing identification of driver oncogenic alterations and progress of targeted therapies addresses the need of comprehensive alternatives to standard molecular methods. The translation into clinical practice of next-generation sequencing (NGS) panels is actually challenged by the compliance of high quality standards for clinical accreditation. Herein, we present the analytical and clinical feasibility study of a hybridization capture-based NGS panel (Action OncoKitDx) for the analysis of somatic mutations, copy number variants (CNVs), fusions, pharmacogenetic SNPs and Microsatellite Instability (MSI) determination in formalin-fixed paraffin-embedded (FFPE) tumor samples. A total of 64 samples were submitted to extensive analytical validation for the identification of previously known variants. An additional set of 166 tumor and patient-matched normal samples were sequenced to assess the clinical utility of the assay across different tumor types. The panel demonstrated good specificity, sensitivity, reproducibility, and repeatability for the identification of all biomarkers analyzed and the 5% limit of detection set was validated. Among the clinical cohorts, the assay revealed pathogenic genomic alterations in 97% of patient cases, and in 82.7%, at least one clinically relevant variant was detected. The validation of accuracy and robustness of this assay supports the Action OncoKitDx’s utility in adult solid tumors.
publishDate 2021
dc.date.none.fl_str_mv 2021
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/11441/116128
https://doi.org/10.3390/jpm11050360
url https://hdl.handle.net/11441/116128
https://doi.org/10.3390/jpm11050360
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Journal of personalized medicine, 11 (5)
https://www.mdpi.com/journal/jpm
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv reponame:idUS. Depósito de Investigación de la Universidad de Sevilla
instname:Universidad de Sevilla (US)
instname_str Universidad de Sevilla (US)
reponame_str idUS. Depósito de Investigación de la Universidad de Sevilla
collection idUS. Depósito de Investigación de la Universidad de Sevilla
repository.name.fl_str_mv
repository.mail.fl_str_mv
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