A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples.

Autor: Esteve-Codina A; CNAG-CRG,Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF), Barcelona, Spain., Arpi O; Cancer Research Program, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain., Martinez-García M; Medical Oncology, Hospital del Mar, Barcelona, Spain., Pineda E; Medical Oncology, Hospital Clínic, Barcelona, Spain., Mallo M; Institut de Recerca Contra la Leucèmia Josep Carreras, Badalona, Barcelona, Spain., Gut M; Sequencing Unit, CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF), Barcelona, Spain., Carrato C; Pathology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain., Rovira A; Cancer Research Program, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain., Lopez R; Pathology Department, Hospital Josep Trueta, Girona, Spain., Tortosa A; 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., Dabad M; CNAG-CRG,Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF), Barcelona, Spain., Del Barco S; Medical Oncology, Institut Català Oncologia (ICO), Hospital Josep Trueta, Girona, Spain., Heath S; CNAG-CRG,Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Universitat Pompeu Fabra (UPF), Barcelona, Spain., Bagué S; Pathology Department, Hospital de Sant Pau, Barcelona, Spain., Ribalta T; Pathology Department (Neuropathology), Hospital Clinic, Barcelona, Spain., Alameda F; Pathology Department, Hospital del Mar, Barcelona, Spain., de la Iglesia N; 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., Balaña C; Institut Català d'Oncologia, Medical Oncology Service, Hospital Germans Trias i Pujol, Badalona, Spain.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2017 Jan 25; Vol. 12 (1), pp. e0170632. Date of Electronic Publication: 2017 Jan 25 (Print Publication: 2017).
DOI: 10.1371/journal.pone.0170632
Abstrakt: 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.
Competing Interests: The authors have declared that no competing interests exist.
Databáze: MEDLINE
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