Direct comparison of microarray gene expression profiles between non-amplification and a modified cDNA amplification procedure applicable for needle biopsy tissues
Direct comparison of microarray gene expression profiles between non-amplification and a modified cDNA amplification procedure applicable for needle biopsy tissues
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DOI：
10.1016/s0361-090x(03)00105-3
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发表时间：
2003-01-01
影响因子：
--
通讯作者：
Sarkar, FH
中科院分区：
文献类型：
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作者：
Li, YW;Ali, S;Sarkar, FH
通过 cDNA 微阵列分析进行的全局基因表达谱已被用来发现用于早期诊断各种癌症、对癌症类型进行分类以及预测患者治疗结果的生物标志物。基因表达谱提供的信息可能有助于设计基于分子机制的癌症预防和/或治疗策略。然而，cDNA 微阵列分析的标准程序需要 5 杯优质总 RNA 作为每个靶标制备反应的起始材料。因此，针活检样本、激光捕获显微解剖组织或流式分选细胞成功利用微阵列技术存在限制。为了分析针吸活检组织的基因表达，我们修改了标准方案，在 cDNA 合成后进行 cDNA 扩增。我们比较了通过标准微阵列方案（cDNA 非扩增方法）和我们的修改方案（cDNA 扩增方法）处理的针活检样品中存在调用、缺席调用的百分比、再现性和一致性。结果表明，cDNA扩增方法具有较高的重现性、代表性，并且与标准cDNA非扩增方法具有较高的一致性。我们使用改进的方法成功地分析了针吸活检组织的基因表达谱，而没有显着改变表达谱。这些结果表明，通过我们的改进方法可以实现小活检样本的全局基因表达谱，以促进临床应用的基因表达谱分析。 (C) 2003 年国际预防肿瘤学会。由爱思唯尔有限公司出版。保留所有权利。
Global gene expression profiling by cDNA microarray analysis has been used to discover the biomarkers for early diagnosis of various cancers, subclassing cancer type, and prediction of patient's treatment outcome. The information provided by gene expression profiling may contribute to the design of molecular mechanism-based strategies for cancer prevention and/or treatment. However, the standard procedure for cDNA microarray analysis requires 5 mug of good quality total RNA as starting material for each target preparation reaction. Thus, there is a limit for needle biopsy samples, laser capture microdissected tissues, or flow-sorted cells to successfully utilize the microarray technology. In order to profile the gene expression of needle biopsy tissue, we have modified the standard protocol by carrying out cDNA amplification after cDNA synthesis. We compared percentage present calls, absent calls, reproducibility, and concordance in needle biopsy samples processed by standard microarray protocol (cDNA non-amplification method) and our modified protocol (cDNA amplification method). The results showed that cDNA amplification method provided high reproducibility, representation, and concordance with the standard cDNA non-amplification method. We have successfully analyzed the gene expression profiles of needle biopsy tissues using the modified method without significantly changing the expression profiles. These results suggest that the global gene expression profiles of small biopsy samples can be achieved by our modified method to facilitate the analysis of gene expression profiles for clinical application. (C) 2003 International Society for Preventive Oncology. Published by Elsevier Ltd. All rights reserved.