title: A set of external reference controls/probes that enable quality assurance between different microarray platforms.
abstract: RNA external standards, although important to ensure equivalence across many microarray platforms, have yet to be fully implemented in the research community. In this article, a set of unique RNA external standards (or RNA standards) and probe pairs that were added to total RNA in the samples before amplification and labeling are described. Concentration-response curves of RNA external standards were used across multiple commercial DNA microarray platforms and/or quantitative real-time polymerase chain reaction (RT-PCR) and next-generation sequencing to identify problematic assays and potential sources of variation in the analytical process. A variety of standards can be added in a range of concentrations spanning high and low abundances, thereby enabling the evaluation of assay performance across the expected range of concentrations found in a clinical sample. Using this approach, we show that we are able to confirm the dynamic range and the limit of detection for each DNA microarray platform, RT-PCR protocol, and next-generation sequencer. In addition, the combination of a series of standards and their probes was investigated on each platform, demonstrating that multiplatform calibration and validation is possible.
authors.affiliation: New Projects Development Division, Toray Industries, Inc., Kamakura, Kanagawa 248-8555, Japan. Electronic address: hideo_akiyama@nts.toray.co.jp.
authors.forename: Hideo
authors.initials: H
authors.lastname: Akiyama
authors.affiliation: New Projects Development Division, Toray Industries, Inc., Kamakura, Kanagawa 248-8555, Japan.
authors.forename: Yoji
authors.initials: Y
authors.lastname: Ueda
authors.affiliation: New Projects Development Division, Toray Industries, Inc., Kamakura, Kanagawa 248-8555, Japan.
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Nobumasa
authors.affiliation: Yokohama Research Laboratories, Mitsubishi Rayon Co. Ltd., Yokohama, Kanagawa 230-0053, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Ooshima
authors.affiliation: DNA Chip Research Inc., Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Yohei
authors.initials: Y
authors.lastname: Ishizawa
authors.affiliation: Technical Research Laboratory, Kurabo Industries Ltd., Neyagawa, Osaka 572-0823, Japan.
authors.forename: Koji
authors.initials: K
authors.lastname: Kitahiro
authors.affiliation: Technical Research Laboratory, Kurabo Industries Ltd., Neyagawa, Osaka 572-0823, Japan.
authors.forename: Isao
authors.initials: I
authors.lastname: Miyagawa
authors.affiliation: Hokkaido System Science Co. Ltd., Sapporo, Hokkaido 001-0932, Japan.
authors.forename: Kazufumi
authors.initials: K
authors.lastname: Watanabe
authors.affiliation: S-BIO Business Division, Sumitomo Bakelite Co. Ltd., Amagasaki, Hyogo 661-8588, Japan.
authors.forename: Takazumi
authors.initials: T
authors.lastname: Nakamura
authors.affiliation: Department of Bio Research, Kamakura Techno-Science, Inc., Kamakura, Kanagawa 248-0036, Japan.
authors.forename: Ritsuka
authors.initials: R
authors.lastname: Tanaka
authors.affiliation: Japan Multiplex bio-Analysis Consortium (JMAC), Chiyoda-ku, Tokyo 102-0083, Japan.
authors.forename: Nobuko
authors.initials: N
authors.lastname: Yamamoto
authors.affiliation: Japan Multiplex bio-Analysis Consortium (JMAC), Chiyoda-ku, Tokyo 102-0083, Japan.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Nakae
authors.affiliation: Graduate School of Biomedical Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan.
authors.forename: Mitsuo
authors.initials: M
authors.lastname: Kawase
authors.affiliation: Ricoh Institute of Technology, Ricoh Company, Ltd., Yokohama, Kanagawa 224-0035, Japan.
authors.forename: Nobuhiro
authors.initials: N
authors.lastname: Gemma
authors.affiliation: Bio-Measurement Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, Ibaraki 305-8566, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Sekiguchi
authors.affiliation: Computational Biology Research Center, Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan.
authors.forename: Wataru
authors.initials: W
authors.lastname: Fujibuchi
authors.affiliation: DNA Chip Research Inc., Yokohama, Kanagawa 230-0045, Japan. Electronic address: matoba@dna-chip.co.jp.
authors.forename: Ryo
authors.initials: R
authors.lastname: Matoba
mesh_terms: D008956:Models, Chemical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards*; D015347:RNA Probes / Q000737:chemistry*; D012015:Reference Standards
chemical_list: D015347:RNA Probes
keywords: Cross-platform; DNA microarray; Dynamic range; External RNA standards; Multiplatform calibration