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Validation and clinical application of a targeted next-generation sequencing gene panel for solid and hematologic malignancies

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dc.contributor.author Prieto-Potin, Iván
dc.contributor.author Carvajal, Nerea
dc.contributor.author Plaza-Sánchez, Jenifer
dc.contributor.author Manso, Rebeca
dc.contributor.author Aúz-Alexandre, Carmen Laura
dc.contributor.author Chamizo, Cristina
dc.contributor.author Zazo, Sandra
dc.contributor.author López-Sánchez, Almudena
dc.contributor.author Rodríguez-Pinilla, Socorro María
dc.contributor.author Camacho Díaz, Laura
dc.contributor.author Longarón Rozalen, Raquel
dc.contributor.author Bellosillo Paricio, Beatriz
dc.contributor.author Somoza, Rosa
dc.contributor.author Hernández-Losa, Javier
dc.contributor.author Fernández-Soria, Víctor Manuel
dc.contributor.author Ramos-Ruiz, Ricardo
dc.contributor.author Cristóbal, Ion
dc.contributor.author García-Foncillas, Jesús
dc.contributor.author Rojo, Federico
dc.date.accessioned 2022-01-28T08:01:04Z
dc.date.available 2022-01-28T08:01:04Z
dc.date.issued 2020
dc.identifier.citation Prieto-Potin I, Carvajal N, Plaza-Sánchez J, Manso R, Aúz-Alexandre CL, Chamizo C, et al. Validation and clinical application of a targeted next-generation sequencing gene panel for solid and hematologic malignancies. PeerJ. 2020 Oct 6; 8: e10069. DOI: 10.7717/peerj.10069
dc.identifier.issn 2167-8359
dc.identifier.uri http://hdl.handle.net/10230/52348
dc.description.abstract Background: Next-generation sequencing (NGS) is a high-throughput technology that has become widely integrated in molecular diagnostics laboratories. Among the large diversity of NGS-based panels, the Trusight Tumor 26 (TsT26) enables the detection of low-frequency variants across 26 genes using the MiSeq platform. Methods: We describe the inter-laboratory validation and subsequent clinical application of the panel in 399 patients presenting a range of tumor types, including gastrointestinal (GI, 29%), hematologic (18%), lung (13%), gynecological and breast (8% each), among others. Results: The panel is highly accurate with a test sensitivity of 92%, and demonstrated high specificity and positive predictive values (95% and 96%, respectively). Sequencing testing was successful in two-thirds of patients, while the remaining third failed due to unsuccessful quality-control filtering. Most detected variants were observed in the TP53 (28%), KRAS (16%), APC (10%) and PIK3CA (8%) genes. Overall, 372 variants were identified, primarily distributed as missense (81%), stop gain (9%) and frameshift (7%) altered sequences and mostly reported as pathogenic (78%) and variants of uncertain significance (19%). Only 14% of patients received targeted treatment based on the variant determined by the panel. The variants most frequently observed in GI and lung tumors were: KRAS c.35G > A (p.G12D), c.35G > T (p.G12V) and c.34G > T (p.G12C). Conclusions: Prior panel validation allowed its use in the laboratory daily practice by providing several relevant and potentially targetable variants across multiple tumors. However, this study is limited by high sample inadequacy rate, raising doubts as to continuity in the clinical setting.
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher PeerJ Inc.
dc.rights Copyright © 2020 Prieto-Potin et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, https://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.title Validation and clinical application of a targeted next-generation sequencing gene panel for solid and hematologic malignancies
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.7717/peerj.10069
dc.subject.keyword Cancer
dc.subject.keyword Hematological malignancies
dc.subject.keyword Next-generation sequencing
dc.subject.keyword Solid tumor
dc.subject.keyword Validation
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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