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

Stefan Graw; Richard Meier; Kay Minn; Clark Bloomer; Andrew K. Godwin; Brooke Fridley; Anda Vlad; Peter Beyerlein; Jeremy Chien

doi:10.1038/srep12335

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

Stefan Graw, Richard Meier, Kay Minn, Clark Bloomer, Andrew K. Godwin, Brooke Fridley, Anda Vlad, Peter Beyerlein, Jeremy Chien

Research output: Contribution to journal › Article › peer-review

42 Scopus citations

Abstract

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.

Original language	English (US)
Article number	12335
Journal	Scientific reports
Volume	5
DOIs	https://doi.org/10.1038/srep12335
State	Published - Jul 23 2015
Externally published	Yes

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title = "Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples",

abstract = "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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AU - Godwin, Andrew K.

AU - Fridley, Brooke

AU - Vlad, Anda

AU - Beyerlein, Peter

AU - Chien, Jeremy

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N2 - 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.

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

Abstract

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