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

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...

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Autores principales: Esteve-Codina, Anna, Arpi, Oriol, Martinez-García, Maria, Pineda, Estela, Mallo, Mar, Gut, Marta, Carrato, Cristina, Rovira, Anna, Lopez, Raquel, Tortosa, Avelina, Dabad, Marc, Del Barco, Sonia, Heath, Simon, Bagué, Silvia, Ribalta, Teresa, Alameda, Francesc, de la Iglesia, Nuria, Balaña, Carmen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5266269/
https://www.ncbi.nlm.nih.gov/pubmed/28122052
http://dx.doi.org/10.1371/journal.pone.0170632
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author Esteve-Codina, Anna
Arpi, Oriol
Martinez-García, Maria
Pineda, Estela
Mallo, Mar
Gut, Marta
Carrato, Cristina
Rovira, Anna
Lopez, Raquel
Tortosa, Avelina
Dabad, Marc
Del Barco, Sonia
Heath, Simon
Bagué, Silvia
Ribalta, Teresa
Alameda, Francesc
de la Iglesia, Nuria
Balaña, Carmen
author_facet Esteve-Codina, Anna
Arpi, Oriol
Martinez-García, Maria
Pineda, Estela
Mallo, Mar
Gut, Marta
Carrato, Cristina
Rovira, Anna
Lopez, Raquel
Tortosa, Avelina
Dabad, Marc
Del Barco, Sonia
Heath, Simon
Bagué, Silvia
Ribalta, Teresa
Alameda, Francesc
de la Iglesia, Nuria
Balaña, Carmen
author_sort Esteve-Codina, Anna
collection PubMed
description 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.
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spelling pubmed-52662692017-02-17 A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples Esteve-Codina, Anna Arpi, Oriol Martinez-García, Maria Pineda, Estela Mallo, Mar Gut, Marta Carrato, Cristina Rovira, Anna Lopez, Raquel Tortosa, Avelina Dabad, Marc Del Barco, Sonia Heath, Simon Bagué, Silvia Ribalta, Teresa Alameda, Francesc de la Iglesia, Nuria Balaña, Carmen PLoS One Research Article 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. Public Library of Science 2017-01-25 /pmc/articles/PMC5266269/ /pubmed/28122052 http://dx.doi.org/10.1371/journal.pone.0170632 Text en © 2017 Esteve-Codina et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Esteve-Codina, Anna
Arpi, Oriol
Martinez-García, Maria
Pineda, Estela
Mallo, Mar
Gut, Marta
Carrato, Cristina
Rovira, Anna
Lopez, Raquel
Tortosa, Avelina
Dabad, Marc
Del Barco, Sonia
Heath, Simon
Bagué, Silvia
Ribalta, Teresa
Alameda, Francesc
de la Iglesia, Nuria
Balaña, Carmen
A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples
title A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples
title_full A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples
title_fullStr A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples
title_full_unstemmed A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples
title_short A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples
title_sort comparison of rna-seq results from paired formalin-fixed paraffin-embedded and fresh-frozen glioblastoma tissue samples
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5266269/
https://www.ncbi.nlm.nih.gov/pubmed/28122052
http://dx.doi.org/10.1371/journal.pone.0170632
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