Comparison of Nanostring nCounter® Data on FFPE Colon Cancer Samples and Affymetrix Microarray Data on Matched Frozen Tissues

Xi Chen, Natasha G Deane, Keeli B Lewis, Jiang Li, Jing Zhu, M Kay Washington, R Daniel Beauchamp, Xi Chen, Natasha G Deane, Keeli B Lewis, Jiang Li, Jing Zhu, M Kay Washington, R Daniel Beauchamp

Abstract

The prognosis of colorectal cancer (CRC) stage II and III patients remains a challenge due to the difficulties of finding robust biomarkers suitable for testing clinical samples. The majority of published gene signatures of CRC have been generated on fresh frozen colorectal tissues. Because collection of frozen tissue is not practical for routine surgical pathology practice, a clinical test that improves prognostic capabilities beyond standard pathological staging of colon cancer will need to be designed for formalin-fixed paraffin-embedded (FFPE) tissues. The NanoString nCounter® platform is a gene expression analysis tool developed for use with FFPE-derived samples. We designed a custom nCounter® codeset based on elements from multiple published fresh frozen tissue microarray-based prognostic gene signatures for colon cancer, and we used this platform to systematically compare gene expression data from FFPE with matched microarray array data from frozen tissues. Our results show moderate correlation of gene expression between two platforms and discovery of a small subset of genes as candidate biomarkers for colon cancer prognosis that are detectable and quantifiable in FFPE tissue sections.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1. Histograms for nCounter and microarray.
Fig 1. Histograms for nCounter and microarray.
The frequency of gene probes (414 elements total) is graphed against median normalized expression values across the x-axis.
Fig 2. The heatmap of pairwise correlations…
Fig 2. The heatmap of pairwise correlations between individual matched FFPE and fresh frozen samples.
X-axis represents the fresh frozen samples and y-axis represents matched FFPE samples.
Fig 3. The histogram of gene-wise correlations…
Fig 3. The histogram of gene-wise correlations between FFPE and fresh frozen samples.
X-axis represents Pearson correlation of each of 414 genes between fresh frozen samples and FFPE samples and y-axis represents the frequency.
Fig 4. Scatterplot of log2 fold change.
Fig 4. Scatterplot of log2 fold change.
Log2 fold change in tumor to normal signal intensity for 414 genes comparing results from nCounter (x-axis) and microarray (y-axis). The red, green and blue dots represent 76, 90 and 248 genes significantly differentially expressed in both, either, and neither platforms respectively.
Fig 5. Scatterplot of log hazard ratio.
Fig 5. Scatterplot of log hazard ratio.
Log hazard ratio for tumor to normal signal intensity for 414 genes vs. overall survival outcomes comparing results from nCounter (x-axis) and microarray (y-axis). The red, green and blue dots represent 6, 49 and 359 genes significantly associated with survival outcomes in both, either, and neither platforms respectively.

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