Boeckx Carolien, Wouters An, Pauwels Bea, Deschoolmeester Vanessa, Specenier Pol, Lukaszuk Krzysztof, Vermorken Jan B, Pauwels Patrick, Peeters Marc, Lardon Filip, Baay Marc F D
Center for Oncological Research Antwerp, Laboratory of Cancer Research and Clinical Oncology, University of Antwerp, Wilrijk, Belgium.
Diagn Mol Pathol. 2011 Dec;20(4):203-11. doi: 10.1097/PDM.0b013e3182230937.
Formalin-fixed paraffin-embedded (FFPE) tissue is the most common tissue specimen widely available. Moreover, long clinical follow-up is on hand. Therefore, FFPE material is a precious source of material for identifying predictive and/or prognostic biomarkers in cancer research on the basis of gene expression. However, the main drawback of FFPE tissue is the significant reduction in quantity and quality of the extracted RNA. The aim of this study is the comparison of different commercially available kits for the RNA isolation in FFPE tissue material.
Five commercially available RNA isolation kits were tested and the concentration, purity, integrity, and raw cycle threshold values were determined.
The mean total RNA concentrations were as follows: Qiagen 25957±19417 ng, Ambion 8249±2898 ng, SA Biosciences 8070±3700 ng, and Macherey-Nagel 622±394 ng. The mean A260/A280 ratios were as follows: Qiagen: 1.81, SA Biosciences: 0.66, Ambion: 1.03, and Macherey-Nagel: 1.04. The mean A260/A230 ratios were as follows: Qiagen: 1.88, SA Biosciences: 1.61, Ambion: 1.54, and Macherey-Nagel: 1.88. The RNA extractions from Epicentre could not be measured by the Nanodrop and, therefore, were excluded from further analysis. The mean RNA integrity number (range, 2.09 to 2.47) and the mean raw cycle threshold values (range, 33.43 to 35.37) were more or less the same for all the tested RNA isolation kits.
Altogether, on the basis of the number of adequate isolations, the kit from Qiagen seems to be the most appropriate kit to be used in our further studies that require RNA isolation from FFPE material.
福尔马林固定石蜡包埋（FFPE）组织是最常见且广泛可得的组织标本。此外，有长期的临床随访数据。因此，FFPE材料是癌症研究中基于基因表达鉴定预测性和/或预后生物标志物的宝贵材料来源。然而，FFPE组织的主要缺点是提取的RNA在数量和质量上显著降低。本研究的目的是比较不同市售试剂盒用于从FFPE组织材料中分离RNA的效果。
测试了五种市售RNA分离试剂盒，并测定了其浓度、纯度、完整性和原始循环阈值。
平均总RNA浓度如下：Qiagen为25957±19417 ng，Ambion为8249±2898 ng，SA Biosciences为8070±3700 ng，Macherey-Nagel为622±394 ng。平均A260/A280比值如下：Qiagen为1.81，SA Biosciences为0.66，Ambion为1.03，Macherey-Nagel为1.04。平均A260/A230比值如下：Qiagen为1.88，SA Biosciences为1.61，Ambion为1.54，Macherey-Nagel为1.88。来自Epicentre的RNA提取物无法用Nanodrop测量，因此被排除在进一步分析之外。所有测试的RNA分离试剂盒的平均RNA完整性数值（范围为2.09至2.47）和平均原始循环阈值（范围为33.43至35.37）大致相同。
总体而言，基于成功分离的次数，Qiagen试剂盒似乎是最适合用于我们进一步研究的试剂盒，这些研究需要从FFPE材料中分离RNA。
