title: A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples.
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.
authors.affiliation: CNAG-CRG,Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Anna
authors.initials: A
authors.lastname: Esteve-Codina
authors.affiliation: Cancer Research Program, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain.
authors.forename: Oriol
authors.initials: O
authors.lastname: Arpi
authors.affiliation: Medical Oncology, Hospital del Mar, Barcelona, Spain.
authors.forename: Maria
authors.initials: M
authors.lastname: Martinez-García
authors.affiliation: Medical Oncology, Hospital Clínic, Barcelona, Spain.
authors.forename: Estela
authors.initials: E
authors.lastname: Pineda
authors.affiliation: Institut de Recerca Contra la Leucèmia Josep Carreras, Badalona, Barcelona, Spain.
authors.forename: Mar
authors.initials: M
authors.lastname: Mallo
authors.affiliation: Sequencing Unit, CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Gut
authors.affiliation: Pathology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain.
authors.forename: Cristina
authors.initials: C
authors.lastname: Carrato
authors.affiliation: Cancer Research Program, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain.
authors.forename: Anna
authors.initials: A
authors.lastname: Rovira
authors.affiliation: Pathology Department, Hospital Josep Trueta, Girona, Spain.
authors.forename: Raquel
authors.initials: R
authors.lastname: Lopez
authors.affiliation: Laboratori de quimio-resistència i cáncer, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Departament Infermeria Fonamental, Institut d'Investigacio Biomedica de Bellvitge (IDIBELL), Bellvitge, Barcelona, Spain.
authors.forename: Avelina
authors.initials: A
authors.lastname: Tortosa
authors.affiliation: CNAG-CRG,Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Marc
authors.initials: M
authors.lastname: Dabad
authors.affiliation: Medical Oncology, Institut Català Oncologia (ICO), Hospital Josep Trueta, Girona, Spain.
authors.forename: Sonia
authors.initials: S
authors.lastname: Del Barco
authors.affiliation: CNAG-CRG,Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Simon
authors.initials: S
authors.lastname: Heath
authors.affiliation: Pathology Department, Hospital de Sant Pau, Barcelona, Spain.
authors.forename: Silvia
authors.initials: S
authors.lastname: Bagué
authors.affiliation: Pathology Department (Neuropathology), Hospital Clinic, Barcelona, Spain.
authors.forename: Teresa
authors.initials: T
authors.lastname: Ribalta
authors.affiliation: Pathology Department, Hospital del Mar, Barcelona, Spain.
authors.forename: Francesc
authors.initials: F
authors.lastname: Alameda
authors.affiliation: Glioma and Neural Stem Cell Group, Translational Genomics and Targeted Therapeutics in Solid Tumors Team, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.
authors.forename: Nuria
authors.initials: N
authors.lastname: de la Iglesia
authors.affiliation: Institut Català d'Oncologia, Medical Oncology Service, Hospital Germans Trias i Pujol, Badalona, Spain.
authors.forename: Carmen
authors.identifier: http://orcid.org/0000-0003-0771-0390
authors.initials: C
authors.lastname: Balaña
mesh_terms: D001932:Brain Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D019295:Computational Biology; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D005909:Glioblastoma / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans