use of non-amplified rna samples for microarray analysis of gene expression使用non-amplified rna样本微阵列基因表达分析.pdfVIP

Use of Non-Amplified RNA Samples for Microarray Analysis of Gene Expression Hiroko Sudo*, Atsuko Mizoguchi, Junpei Kawauchi, Hideo Akiyama, Satoko Takizawa New Frontiers Research Laboratories, Toray Industries, Inc., Kamakura, Kanagawa, Japan Abstract Demand for high quality gene expression data has driven the development of revolutionary microarray technologies. The quality of the data is affected by the performance of the microarray platform as well as how the nucleic acid targets are prepared. The most common method for target nucleic acid preparation includes in vitro transcription amplification of the sample RNA. Although this method requires a small amount of starting material and is reported to have high reproducibility, there are also technical disadvantages such as amplification bias and the long, laborious protocol. Using RNA derived from human brain, breast and colon, we demonstrate that a non-amplification method, which was previously shown to be inferior, could be transformed to a highly quantitative method with a dynamic range of five orders of magnitude. Furthermore, the correlation coefficient calculated by comparing microarray assays using non-amplified samples with qRT- PCR assays was approximately 0.9, a value much higher than when samples were prepared using amplification methods. Our results were also compared with data from various microarray platforms studied in the MicroArray Quality Control (MAQC) project. In combination with micro-columnar 3D-GeneTM microarray, this non-amplification method is applicable to a variety of genetic analyses, including biomarker screening and diagnostic tests for cancer. Citation: Sudo H, Mizoguchi A, Kawauchi J, Akiyama H, Takizawa S (2012) Use of Non-Amplified RNA Samples for Microarray Analysis of Gene Expression. PLoS ONE 7(2): e31397. doi:10.1371/jou