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

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.

DOI: 10.1038/srep33273

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@inproceedings{Zhu2016EvaluationOF, title={Evaluation of frozen tissue-derived prognostic gene expression signatures in FFPE colorectal cancer samples}, author={Jing Zhu and Natasha G. Deane and Keeli B. Lewis and Chandrasekhar Padmanabhan and M. Kay Washington and Kristen K Ciombor and Cynthia Dawn Timmers and Richard M. Goldberg and Robert Daniel Beauchamp and Xi Chen}, booktitle={Scientific reports}, year={2016} }