Evaluation of frozen tissue-derived prognostic gene expression signatures in FFPE colorectal cancer samples

Jing Zhu, Natasha G. Deane, Keeli B. Lewis, Chandrasekhar Padmanabhan, M. Kay Washington, Kristen K. Ciombor, Cynthia Timmers, Richard M. Goldberg, R. Daniel Beauchamp, Xi Chen

Research output: Contribution to journalArticle

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Abstract

Defining molecular features that can predict the recurrence of colorectal cancer (CRC) for stage II-III patients remains challenging in cancer research. Most available clinical samples are Formalin-Fixed, Paraffin-Embedded (FFPE). NanoString nCounter® and Affymetrix GeneChip® Human Transcriptome Array 2.0 (HTA) are the two platforms marketed for high-throughput gene expression profiling for FFPE samples. In this study, to evaluate the gene expression of frozen tissue-derived prognostic signatures in FFPE CRC samples, we evaluated the expression of 516 genes from published frozen tissue-derived prognostic signatures in 42 FFPE CRC samples measured by both platforms. Based on HTA platform-derived data, we identified both gene (99 individual genes, FDR < 0.05) and gene set (four of the six reported multi-gene signatures with sufficient information for evaluation, P < 0.05) expression differences associated with survival outcomes. Using nCounter platform-derived data, one of the six multi-gene signatures (P < 0.05) but no individual gene was associated with survival outcomes. Our study indicated that sufficiently high quality RNA could be obtained from FFPE tumor tissues to detect frozen tissue-derived prognostic gene expression signatures for CRC patients.

Original languageEnglish (US)
Article number33273
JournalScientific Reports
Volume6
DOIs
StatePublished - Sep 14 2016

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Transcriptome
Paraffin
Formaldehyde
Colorectal Neoplasms
Genes
Gene Expression
Survival
Gene Expression Profiling
Neoplasms
RNA
Recurrence
Research

ASJC Scopus subject areas

  • General

Cite this

Evaluation of frozen tissue-derived prognostic gene expression signatures in FFPE colorectal cancer samples. / Zhu, Jing; Deane, Natasha G.; Lewis, Keeli B.; Padmanabhan, Chandrasekhar; Washington, M. Kay; Ciombor, Kristen K.; Timmers, Cynthia; Goldberg, Richard M.; Beauchamp, R. Daniel; Chen, Xi.

In: Scientific Reports, Vol. 6, 33273, 14.09.2016.

Research output: Contribution to journalArticle

Zhu, J, Deane, NG, Lewis, KB, Padmanabhan, C, Washington, MK, Ciombor, KK, Timmers, C, Goldberg, RM, Beauchamp, RD & Chen, X 2016, 'Evaluation of frozen tissue-derived prognostic gene expression signatures in FFPE colorectal cancer samples', Scientific Reports, vol. 6, 33273. https://doi.org/10.1038/srep33273
Zhu, Jing ; Deane, Natasha G. ; Lewis, Keeli B. ; Padmanabhan, Chandrasekhar ; Washington, M. Kay ; Ciombor, Kristen K. ; Timmers, Cynthia ; Goldberg, Richard M. ; Beauchamp, R. Daniel ; Chen, Xi. / Evaluation of frozen tissue-derived prognostic gene expression signatures in FFPE colorectal cancer samples. In: Scientific Reports. 2016 ; Vol. 6.
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