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

Zhu J, Deane NG, Lewis KB, Padmanabhan C, Washington MK, Ciombor KK, Timmers C, Goldberg RM, Beauchamp RD, Chen X
Sci Rep. 2016 6: 33273

PMID: 27623752 · PMCID: PMC5021945 · DOI:10.1038/srep33273

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.

MeSH Terms (13)

Colorectal Neoplasms Disease-Free Survival Female Formaldehyde Gene Expression Regulation, Neoplastic Humans Male Neoplasm Recurrence, Local Oligonucleotide Array Sequence Analysis Paraffin Embedding Prognosis Tissue Fixation Transcriptome

Connections (2)

This publication is referenced by other Labnodes entities: