Files

669634.pdf (2 MB)

Document type

Article

Version

Published version

Publication date

2017-01-25

Publication license

cc-by (c) Esteve-Codina, Anna et al., 2017
Please use this identifier to cite or link to this item: https://hdl.handle.net/2445/108650

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

Journal Title

Authors

Director/Tutor

Additional contribution

Journal ISSN

Volume Title

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.

Related resource

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

Subject

RNA, Genètica, Mapatge cromosòmic humà

Subject (English)

RNA, Genetics, Human gene mapping

Citation

Collections

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))

Citation

ESTEVE CODINA, Anna, et al. A comparison of RNA-Seq results from paired formalin-fixed paraffin-embedded and fresh-frozen glioblastoma tissue samples. PLoS One. 2017. Vol. 12, num. 1, pags. e0170632. ISSN 1932-6203. [consulted: 7 of October of 2026]. Available at: https://hdl.handle.net/2445/108650

Export metadata

JSON - METS

Share record