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2017-01-25

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cc-by (c) Esteve-Codina, Anna et al., 2017
Si us plau utilitzeu sempre aquest identificador per citar o enllaçar aquest document: https://hdl.handle.net/2445/108650

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

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https://doi.org/10.1371/journal.pone.0170632

Resum

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.

Matèries

RNA, Genètica, Mapatge cromosòmic humà

Matèries (anglès)

RNA, Genetics, Human gene mapping

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Col·leccions

Articles publicats en revistes (Fonaments Clínics)
Articles publicats en revistes (IDIBAPS: Institut d'investigacions Biomèdiques August Pi i Sunyer)
Articles publicats en revistes (Infermeria Fonamental i Clínica)
Articles publicats en revistes (Institut d'lnvestigació Biomèdica de Bellvitge (IDIBELL))

Citació

ESTEVE CODINA, Anna, ARPI, Oriol, MARTÍNEZ-GARCÍA, María, PINEDA, Estela, MALLO, Mar, GUT, Marta, CARRATO, Cristina, ROVIRA, Anna, LÓPEZ, Raquel, TORTOSA I MORENO, Avelina, DABAD, Marc, BARCO, Sonia del, HEATH, Simon c., BAGUÉ, Silvia, RIBALTA FARRÉS, Teresa maría, ALAMEDA, Francesc, IGLESIA, Núria de la, BALAÑA, Carmen, GLIOCAT Group. A comparison of RNA-Seq results from paired formalin-fixed paraffin-embedded and fresh-frozen glioblastoma tissue samples.. _PLoS One_. 2017. Vol. 12, núm. 1, pàgs. e0170632. [consulta: 23 de gener de 2026]. ISSN: 1932-6203. [Disponible a: https://hdl.handle.net/2445/108650]

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