A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples
Esteve-Codina, Anna (Centre de Regulació Genòmica)
Arpí Lluciá, Oriol (Institut Hospital del Mar d'Investigacions Mèdiques)
Martinez-García, Maria (Hospital del Mar (Barcelona, Catalunya))
Pineda, Estela (Hospital Clínic i Provincial de Barcelona)
Mallo, Maria del Mar (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras)
Gut, Marta (Centre de Regulació Genòmica)
Carrato, Cristina (Institut Germans Trias i Pujol. Hospital Universitari Germans Trias i Pujol)
Rovira, Anna (Institut Hospital del Mar d'Investigacions Mèdiques)
Lopez, Raquel (Hospital Universitari de Girona Doctor Josep Trueta)
Tortosa, Avelina (Universitat de Barcelona, Departament d'Infermeria Fonamental)
Dabad, Marc (Centre de Regulació Genòmica)
Del Barco Berrón, Sonia (Institut Català d'Oncologia)
Heath, Simon (Centre de Regulació Genòmica)
Bagué Rosell, Sílvia (Institut d'Investigació Biomèdica Sant Pau)
Ribalta Farres, Teresa (Hospital Clínic i Provincial de Barcelona)
Alameda, Francesc (Hospital del Mar (Barcelona, Catalunya))
de la Iglesia, Nuria (Institut d'Investigacions Biomèdiques August Pi i Sunyer)
Balañá, Carmen (Institut Germans Trias i Pujol. Hospital Universitari Germans Trias i Pujol)
Glioma Catalonia Group (GLIOCAT)
Universitat Autònoma de Barcelona

Date:	2017
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.
Grants:	Ministerio de Economía y Competitividad RTICC/RD12/0036/0044 Agència de Gestió d'Ajuts Universitaris i de Recerca SGR541 Instituto de Salud Carlos III PT13/0001 Instituto de Salud Carlos III PTA2014-09515-I
Note:	Altres ajuts: Fundació La Marató TV3, Project: 665/C/2013
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Published in:	PloS one, 2017, p. 1-18, ISSN 1932-6203

DOI: 10.1371/journal.pone.0170632
PMID: 28122052

18 p, 2.0 MB

The record appears in these collections:
Research literature > UAB research groups literature > Research Centres and Groups (research output) > Health sciences and biosciences > Institut d'Investigació en Ciencies de la Salut Germans Trias i Pujol (IGTP) > Josep Carreras Leukaemia Research Institute
Research literature > UAB research groups literature > Research Centres and Groups (research output) > Health sciences and biosciences > Institut de Recerca Sant Pau
Articles > Research articles
Articles > Published articles