Comparison of Nanostring nCounter® Data on FFPE Colon Cancer Samples and Affymetrix Microarray Data on Matched Frozen Tissues.
Comparison of Nanostring nCounter® Data on FFPE Colon Cancer Samples and Affymetrix Microarray Data on Matched Frozen Tissues.
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DOI：
10.1371/journal.pone.0153784
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Beauchamp RD
中科院分区：
文献类型：
--
作者：
Chen X;Deane NG;Lewis KB;Li J;Zhu J;Washington MK;Beauchamp RD
由于难以找到适用于测试临床样品的稳健生物标志物，II期和III期结直肠癌（CRC）患者的预后仍然是一个挑战。大多数已发表的CRC基因签名是在新鲜冷冻的结直肠组织上产生的。由于冷冻组织的收集对于常规外科病理学实践是不实际的，因此需要针对福尔马林固定石蜡包埋（FFPE）组织设计提高结肠癌标准病理学分期之外的预后能力的临床测试。NanoString nCounter®平台是开发用于FFPE衍生样品的基因表达分析工具。我们设计了一个定制的nCounter®代码集，该代码集基于来自多个已发表的新鲜冷冻组织微阵列的结肠癌预后基因特征的元素，我们使用该平台系统地比较了FFPE的基因表达数据与冷冻组织的匹配微阵列数据。我们的研究结果显示，两个平台之间的基因表达存在中度相关性，并且发现了一小部分基因作为结肠癌预后的候选生物标志物，这些生物标志物在FFPE组织切片中可检测和定量。
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.