Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples

Current genomic studies are limited by the availability of fresh tissue samples. Here, we show that Illumina RNA sequencing of formalin-fixed diagnostic tumor samples produces gene expression that is strongly correlated with matched frozen tumor samples (r > 0.89). In addition, sequence variation...

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Autores principales: Graw, Stefan, Meier, Richard, Minn, Kay, Bloomer, Clark, Godwin, Andrew K., Fridley, Brooke, Vlad, Anda, Beyerlein, Peter, Chien, Jeremy
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2015
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4511951/
https://www.ncbi.nlm.nih.gov/pubmed/26202458
http://dx.doi.org/10.1038/srep12335
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author Graw, Stefan
Meier, Richard
Minn, Kay
Bloomer, Clark
Godwin, Andrew K.
Fridley, Brooke
Vlad, Anda
Beyerlein, Peter
Chien, Jeremy
author_facet Graw, Stefan
Meier, Richard
Minn, Kay
Bloomer, Clark
Godwin, Andrew K.
Fridley, Brooke
Vlad, Anda
Beyerlein, Peter
Chien, Jeremy
author_sort Graw, Stefan
collection PubMed
description Current genomic studies are limited by the availability of fresh tissue samples. Here, we show that Illumina RNA sequencing of formalin-fixed diagnostic tumor samples produces gene expression that is strongly correlated with matched frozen tumor samples (r > 0.89). In addition, sequence variations identified from FFPE RNA show 99.67% concordance with that from exome sequencing of matched frozen tumor samples. Because FFPE is a routine diagnostic sample preparation, the feasibility results reported here will facilitate the setup of large-scale research and clinical studies in medical genomics that are currently limited by the availability of fresh frozen samples.
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spelling pubmed-45119512015-07-28 Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples Graw, Stefan Meier, Richard Minn, Kay Bloomer, Clark Godwin, Andrew K. Fridley, Brooke Vlad, Anda Beyerlein, Peter Chien, Jeremy Sci Rep Article Current genomic studies are limited by the availability of fresh tissue samples. Here, we show that Illumina RNA sequencing of formalin-fixed diagnostic tumor samples produces gene expression that is strongly correlated with matched frozen tumor samples (r > 0.89). In addition, sequence variations identified from FFPE RNA show 99.67% concordance with that from exome sequencing of matched frozen tumor samples. Because FFPE is a routine diagnostic sample preparation, the feasibility results reported here will facilitate the setup of large-scale research and clinical studies in medical genomics that are currently limited by the availability of fresh frozen samples. Nature Publishing Group 2015-07-23 /pmc/articles/PMC4511951/ /pubmed/26202458 http://dx.doi.org/10.1038/srep12335 Text en Copyright © 2015, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Graw, Stefan
Meier, Richard
Minn, Kay
Bloomer, Clark
Godwin, Andrew K.
Fridley, Brooke
Vlad, Anda
Beyerlein, Peter
Chien, Jeremy
Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples
title Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples
title_full Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples
title_fullStr Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples
title_full_unstemmed Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples
title_short Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples
title_sort robust gene expression and mutation analyses of rna-sequencing of formalin-fixed diagnostic tumor samples
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4511951/
https://www.ncbi.nlm.nih.gov/pubmed/26202458
http://dx.doi.org/10.1038/srep12335
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