A set of external reference controls/probes that enable quality assurance between different microarray platforms

Hideo Akiyama, Yoji Ueda, Hitoshi Nobumasa, Hiroyuki Ooshima, Yohei Ishizawa, Koji Kitahiro, Isao Miyagawa, Kazufumi Watanabe, Takazumi Nakamura, Ritsuka Tanaka, Nobuko Yamamoto, Hiroki Nakae, Mitsuo Kawase, Nobuhiro Gemma, Yuji Sekiguchi, Wataru Fujibuchi, Ryo Matoba

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)75-83
Number of pages9
JournalAnalytical Biochemistry
Volume472
DOIs
Publication statusPublished - 2015 Mar 1

Keywords

  • Cross-platform
  • DNA microarray
  • Dynamic range
  • External RNA standards
  • Multiplatform calibration

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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