Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues
Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues
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DOI：
10.1016/j.jmoldx.2015.02.002
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发表时间：
2015-07-01
影响因子：
4.1
通讯作者：
Birrer, Michael
中科院分区：
文献类型：
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作者：
Tyekucheva, Svitlana;Martin, Neil E.;Birrer, Michael
存档福尔马林固定，石蜡包埋（FFPE）组织标本代表了一个现成的，但在很大程度上未开发的资源基因表达谱为基础的生物标志物的发现。已经提出了几种技术来科普与档案标本相关的RNA交联和降解的偏倚，以产生与新鲜冷冻材料中的RNA相当的数据。这些RNA表达平台的直接比较研究仍然很少。我们比较了两种用于前列腺癌和卵巢癌临床研究中存档FFPE标本的RNA表达谱分析的市售平台：使用NuGen WT-Ovation FFPE System V2进行全转录组扩增后的Affytron Human Gene 1.0ST Array和未进行扩增的NanoString nCounter。对于每个检测，我们分析了7个前列腺癌和11个卵巢癌标本，块年龄为4至21岁。两个平台通过FFPE材料的技术重复产生具有高灵敏度和可重复性的基因表达谱。在每个队列中，敏感性和再现性在各年龄组间保持较高。两个平台检测到的基因的转录表达值显示出强烈的一致性。我们显示了两个平台为两个队列生成的特定基因签名的生物学有效性。我们的研究支持使用商业平台对存档的前列腺和卵巢肿瘤标本进行基因表达谱分析和大规模签名验证的可行性。这些方法有可能通过生物标志物的发现和验证来帮助精准医学。
Archival formalin-fixed, paraffin-embedded (FFPE) tissue specimens represent a readily available but largely untapped resource for gene expression profiling based biomarker discovery. Severaltechnologies have been proposed to cope with the bias from RNA cross-linking and degradation associated with archival specimens to generate data comparable with RNA from fresh-frozen materials. Direct comparison studies of these RNA expression platforms remain rare. We compared two commercially available platforms for RNA expression profiling of archival FFPE specimens from clinical studies of prostate and ovarian cancer: the Affymetrix Human Gene 1.0ST Array following whole-transcriptome amplification using the NuGen WT-Ovation FFPE System V2, and the NanoString nCounter without amplification. For each assay, we profiled 7 prostate and 11 ovarian cancer specimens, with a block age of 4 to 21 years. Both platforms produced gene expression profiles with high sensitivity and reproducibility through technical repeats from FFPE materials. Sensitivity and reproducibility remained high across block age within each cohort. A strong concordance was shown for the transcript expression values for genes detected by both platforms. We showed the biological validity of specific gene signatures generated by both platforms for both cohorts. Our study supports the feasibility of gene expression profiling and Large-scale signature validation on archival prostate and ovarian tumor specimens using commercial platforms. These approaches have the potential to aid precision medicine with biomarker discovery and validation.