Esteve-Codina, AnnaArpí Llucià, OriolMartínez-García, MariaPineda, EstelaMallo, MarGut, MartaCarrato, CristinaRovira Guerín, AnaLopez, RaquelTortosa, AvelinaDabad, Marcdel Barco, SoniaHeath, SimonBagué, SilviaRibalta, TeresaAlameda Quitllet, Franciscode la Iglesia, NuriaBalaña, CarmenGLIOCAT Group2018-02-232018-02-232017Esteve-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.01706321932-6203http://hdl.handle.net/10230/33980The 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 preservedapplication/pdfeng© 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.Cervell -- Aspectes genèticsCervell -- Tumorsinfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1371/journal.pone.0170632info:eu-repo/semantics/openAccess