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Sci Rep. 2016 Sep 14;6:33273. doi: 10.1038/srep33273.

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

Author information

1
Vanderbilt University, Department of Surgery, Nashville, 37232, USA.
2
Vanderbilt University, Vanderbilt Ingram Cancer Center, Nashville, 37232, USA.
3
Vanderbilt University, Department of Pathology, Nashville, 37232, USA.
4
The Ohio State University Comprehensive Cancer Center, Columbus, 43210, USA.
5
Ohio State University, Division of Medical Oncology, Department of Internal Medicine, Columbus, 43210, USA.
6
Vanderbilt University, Department of Cell and Developmental Biology, Nashville, 37232, USA.
7
Vanderbilt University, Department of Cancer Biology, Nashville, 37232, USA.
8
University of Miami Miller School of Medicine, Division of Biostatistics, Department of Public Health Sciences, Miami, 33136, USA.
9
University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, 33136, USA.

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.

PMID:
27623752
PMCID:
PMC5021945
DOI:
10.1038/srep33273
[Indexed for MEDLINE]
Free PMC Article

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