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首页> 外文期刊>Genomics >Identification of methods for use of formalin-fixed, paraffin-embedded tissue samples in RNA expression profiling.
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Identification of methods for use of formalin-fixed, paraffin-embedded tissue samples in RNA expression profiling.

机译：鉴定在RNA表达图谱中使用福尔马林固定，石蜡包埋的组织样品的方法。

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摘要

Formalin-fixed paraffin-embedded (FFPE) tissue samples are a potentially valuable resource of expression information for medical research, but are under-utilized due to degradation and modification of the RNA. Using a random primer-based RNA amplification strategy, we have evaluated multiple protocols for the extraction and isolation of RNA from FFPE samples. We found that the RecoverAll RNA isolation procedure with three or four slices (ten-microns in thickness), supplemented with additional DNAse, gave optimal results. RNA integrity as assessed by Agilent Bioanalyzer, and amplification of the 28S ribosomal RNA, were predictive for the number of genes detected on Affymetrix arrays. We obtained expression data for colon and lung tumor and normal FFPE samples and matched frozen samples and found a high correlation between frozen and matched FFPE samples (R(2) between 0.82 and 0.89), while the signature sets in tumor versus normal comparisons were also quite similar. QPCR confirmed all 16 of the differential expression results from the microarrays that we tested. Differentially expressed signature genes from tumor versus matched normal FFPE tissue from colon and lung were identified as cancer-related, with 95 colon tumor and 67 lung tumor genes identified, respectively.
机译：福尔马林固定石蜡包埋（FFPE）组织样品是用于医学研究的表达信息的潜在有价值资源，但由于RNA的降解和修饰而未被充分利用。使用基于随机引物的RNA扩增策略，我们评估了从FFPE样品中提取和分离RNA的多种方案。我们发现，用三或四个切片（厚度为十微米），并辅以额外的DNAse的RecoverAll RNA分离程序可得到最佳结果。通过Agilent Bioanalyzer评估的RNA完整性以及28S核糖体RNA的扩增可预测在Affymetrix阵列上检测到的基因数量。我们获得了结肠和肺部肿瘤以及正常FFPE样品和匹配的冷冻样品的表达数据，发现冷冻和匹配的FFPE样品之间的相关性很高（R（2）在0.82和0.89之间），而肿瘤与正常对照的特征集也是非常相似。 QPCR证实了我们测试的微阵列的所有16个差异表达结果。来自肿瘤的差异表达特征基因与来自结肠和肺的匹配的正常FFPE组织的差异基因被鉴定为与癌症相关，分别鉴定出95个结肠肿瘤和67个肺肿瘤基因。

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