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

Chen X, Deane NG, Lewis KB, Li J, Zhu J, Washington MK, Beauchamp RD
PLoS One. 2016 11 (5): e0153784

PMID: 27176004 · PMCID: PMC4866771 · DOI:10.1371/journal.pone.0153784

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.

MeSH Terms (10)

Colonic Neoplasms Formaldehyde Frozen Sections Gene Expression Regulation, Neoplastic Humans Oligonucleotide Array Sequence Analysis Paraffin Embedding RNA, Neoplasm Survival Analysis Tissue Fixation

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