%0 Journal Article %1 EsteveCodina:2017:PLoS-One:28122052 %A Esteve-Codina, Anna %A Arpi, Oriol %A Martinez-García, Maria %A Pineda, Estela %A Mallo, Mar %A Gut, Marta %A Carrato, Cristina %A Rovira, Anna %A Lopez, Raquel %A Tortosa, Avelina %A Dabad, Marc %A Del Barco, Sonia %A Heath, Simon %A Bagué, Silvia %A Ribalta, Teresa %A Alameda, Francesc %A de la Iglesia, Nuria %A Balaña, Carmen %A on behalf of the GLIOCAT Group, %D 2017 %I Public Library of Science %J PLOS ONE %K MUSTREAD cancer-research comparison ffpe fulltext glioblastoma rna-seq %N 1 %P 1-18 %R 10.1371/journal.pone.0170632 %T A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples %U https://www.ncbi.nlm.nih.gov/pubmed/28122052 %V 12 %X 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.

@article{EsteveCodina:2017:PLoS-One:28122052, 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.}, added-at = {2017-11-03T09:31:28.000+0100}, author = {Esteve-Codina, Anna and Arpi, Oriol and Martinez-García, Maria and Pineda, Estela and Mallo, Mar and Gut, Marta and Carrato, Cristina and Rovira, Anna and Lopez, Raquel and Tortosa, Avelina and Dabad, Marc and Del Barco, Sonia and Heath, Simon and Bagué, Silvia and Ribalta, Teresa and Alameda, Francesc and de la Iglesia, Nuria and Balaña, Carmen and on behalf of the GLIOCAT Group}, biburl = {https://www.bibsonomy.org/bibtex/20e13b02279182c0300d9c16c2d8eec32/marcsaric}, description = {A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples}, doi = {10.1371/journal.pone.0170632}, interhash = {67de9eb4ecbe49cf737cdf6f5caea66f}, intrahash = {0e13b02279182c0300d9c16c2d8eec32}, journal = {PLOS ONE}, keywords = {MUSTREAD cancer-research comparison ffpe fulltext glioblastoma rna-seq}, month = {01}, number = 1, pages = {1-18}, publisher = {Public Library of Science}, timestamp = {2019-06-10T22:57:11.000+0200}, title = {A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples}, url = {https://www.ncbi.nlm.nih.gov/pubmed/28122052}, volume = 12, year = 2017 }