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, Annaca
- dc.contributor.author Arpí Llucià, Oriolca
- dc.contributor.author Martínez-García, Mariaca
- dc.contributor.author Pineda, Estelaca
- dc.contributor.author Mallo, Marca
- dc.contributor.author Gut, Martaca
- dc.contributor.author Carrato, Cristinaca
- dc.contributor.author Rovira Guerín, Anaca
- dc.contributor.author Lopez, Raquelca
- dc.contributor.author Tortosa, Avelinaca
- dc.contributor.author Dabad, Marcca
- dc.contributor.author del Barco, Soniaca
- dc.contributor.author Heath, Simonca
- dc.contributor.author Bagué, Silviaca
- dc.contributor.author Ribalta, Teresaca
- dc.contributor.author Alameda Quitllet, Franciscoca
- dc.contributor.author de la Iglesia, Nuriaca
- dc.contributor.author Balaña, Carmenca
- dc.contributor.author GLIOCAT Groupca
- dc.date.accessioned 2018-02-23T08:59:50Z
- dc.date.available 2018-02-23T08:59:50Z
- dc.date.issued 2017
- 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.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.doi http://dx.doi.org/10.1371/journal.pone.0170632
- dc.identifier.issn 1932-6203
- dc.identifier.uri http://hdl.handle.net/10230/33980
- dc.language.iso eng
- dc.publisher Public Library of Science (PLoS)ca
- 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.rights.accessRights info:eu-repo/semantics/openAccess
- 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 samplesca
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion