A comparison of RNA-Seq results from paired formalin-fixed paraffin-embedded and fresh-frozen glioblastoma tissue samples
| Autor: | Esteve-Codina, Anna, Arpí Lluciá, Oriol, Martinez-García, Maria, Pineda, Estela, Mallo, Maria del Mar, Gut, Marta, Carrato, Cristina, Rovira, Anna, Lopez, Raquel, Tortosa, Avelina, Dabad, Marc, Del Barco Berrón, Sonia, Heath, Simon, Bagué Rosell, Sílvia, Ribalta Farres, Teresa, Alameda, Francesc, de la Iglesia, Nuria, Balañá, Carmen, Glioma Catalonia Group (GLIOCAT), Universitat Autònoma de Barcelona |
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| Přispěvatelé: | Universitat de Barcelona |
| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
cDNA libraries Molecular biology lcsh:Medicine Gene Expression RNA-Seq Bioinformatics Biochemistry Transcriptome Sequencing techniques Gene expression Medicine and Health Sciences Blastomas DNA libraries lcsh:Science Neurological Tumors Energy-Producing Organelles Multidisciplinary Brain Neoplasms High-Throughput Nucleotide Sequencing RNA sequencing Complementary DNA Mitochondria Gene Expression Regulation Neoplastic Nucleic acids Chemistry Oncology Neurology Physical Sciences RNA extraction Cellular Structures and Organelles Research Article Chemical Elements Forms of DNA Mapatge cromosòmic humà Single-nucleotide polymorphism Genomics Biology Bioenergetics 03 medical and health sciences Extraction techniques Cervell -- Tumors Genetics Humans Human gene mapping Biology and life sciences cDNA library Gene Expression Profiling lcsh:R Gene Mapping RNA Computational Biology Cancers and Neoplasms DNA Cell Biology Research and analysis methods 030104 developmental biology Molecular biology techniques Tin Cervell -- Aspectes genètics lcsh:Q Glioblastoma Genètica Glioblastoma Multiforme |
| Zdroj: | Recercat. Dipósit de la Recerca de Catalunya instname PLoS ONE PLoS ONE, Vol 12, Iss 1, p e0170632 (2017) Dipòsit Digital de la UB Universidad de Barcelona PLoS One r-IIB SANT PAU. Repositorio Institucional de Producción Científica del Instituto de Investigación Biomédica Sant Pau r-IGTP. Repositorio Institucional de Producción Científica del Instituto de Investigación Germans Trias i Pujol |
| ISSN: | 1932-6203 |
| Popis: | Altres ajuts: Fundació La Marató TV3, Project: 665/C/2013 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. |
| Databáze: | OpenAIRE |
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