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A comparison of RNA-Seq results from paired formalin-fixed paraffin-embedded and fresh-frozen glioblastoma tissue samples

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dc.contributor.author Esteve-Codina, Anna
dc.contributor.author Arpí Llucià, Oriol
dc.contributor.author Martínez-García, Maria
dc.contributor.author Pineda, Estela
dc.contributor.author Mallo, Mar
dc.contributor.author Gut, Marta
dc.contributor.author Carrato, Cristina
dc.contributor.author Rovira Guerín, Ana
dc.contributor.author Lopez, Raquel
dc.contributor.author Tortosa, Avelina
dc.contributor.author Dabad, Marc
dc.contributor.author del Barco, Sonia
dc.contributor.author Heath, Simon
dc.contributor.author Bagué, Silvia
dc.contributor.author Ribalta, Teresa
dc.contributor.author Alameda Quitllet, Francisco
dc.contributor.author de la Iglesia, Nuria
dc.contributor.author Balaña, Carmen
dc.contributor.author GLIOCAT Group
dc.date.accessioned 2018-02-23T08:59:50Z
dc.date.available 2018-02-23T08:59:50Z
dc.date.issued 2017
dc.identifier.citation Esteve-Codina A, Arpi O, Martinez-García M, Pineda E, Mallo M, Gut M et al. A comparison of RNA-Seq results from paired formalin-fixed paraffin-embedded and fresh-frozen glioblastoma tissue samples. PLoS One. 2017 Jan 25;12(1):e0170632. DOI: 10.1371/journal.pone.0170632
dc.identifier.issn 1932-6203
dc.identifier.uri http://hdl.handle.net/10230/33980
dc.description.abstract The molecular classification of glioblastoma (GBM) based on gene expression might better explain outcome and response to treatment than clinical factors. Whole transcriptome sequencing using next-generation sequencing platforms is rapidly becoming accepted as a tool for measuring gene expression for both research and clinical use. Fresh frozen (FF) tissue specimens of GBM are difficult to obtain since tumor tissue obtained at surgery is often scarce and necrotic and diagnosis is prioritized over freezing. After diagnosis, leftover tissue is usually stored as formalin-fixed paraffin-embedded (FFPE) tissue. However, RNA from FFPE tissues is usually degraded, which could hamper gene expression analysis. We compared RNA-Seq data obtained from matched pairs of FF and FFPE GBM specimens. Only three FFPE out of eleven FFPE-FF matched samples yielded informative results. Several quality-control measurements showed that RNA from FFPE samples was highly degraded but maintained transcriptomic similarities to RNA from FF samples. Certain issues regarding mutation analysis and subtype prediction were detected. Nevertheless, our results suggest that RNA-Seq of FFPE GBM specimens provides reliable gene expression data that can be used in molecular studies of GBM if the RNA is sufficiently preserved
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Public Library of Science (PLoS)
dc.relation.ispartof PLoS One. 2017 Jan 25;12(1):e0170632
dc.rights © 2017 Esteve-Codina et al. This is an open access article distributed under the terms of the https://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.subject.other Cervell -- Aspectes genètics
dc.subject.other Cervell -- Tumors
dc.title A comparison of RNA-Seq results from paired formalin-fixed paraffin-embedded and fresh-frozen glioblastoma tissue samples
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1371/journal.pone.0170632
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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