title: Use of non-amplified RNA samples for microarray analysis of gene expression.
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-Gene™ microarray, this non-amplification method is applicable to a variety of genetic analyses, including biomarker screening and diagnostic tests for cancer.
authors.affiliation: New Frontiers Research Laboratories, Toray Industries, Inc., Kamakura, Kanagawa, Japan. Hiroko_Sudo@nts.toray.co.jp
authors.forename: Hiroko
authors.initials: H
authors.lastname: Sudo
authors.forename: Atsuko
authors.initials: A
authors.lastname: Mizoguchi
authors.forename: Junpei
authors.initials: J
authors.lastname: Kawauchi
authors.forename: Hideo
authors.initials: H
authors.lastname: Akiyama
authors.forename: Satoko
authors.initials: S
authors.lastname: Takizawa
mesh_terms: D001932:Brain Neoplasms / Q000235:genetics* / Q000378:metabolism; D001943:Breast Neoplasms / Q000235:genetics* / Q000378:metabolism; D003110:Colonic Neoplasms / Q000235:genetics* / Q000378:metabolism; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D046228:Microarray Analysis; D021141:Nucleic Acid Amplification Techniques; D011786:Quality Control; D012333:RNA, Messenger / Q000235:genetics; D012334:RNA, Neoplasm / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D012333:RNA, Messenger; D012334:RNA, Neoplasm