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Intra-Platform Repeatability and Inter-Platform Comparability of MicroRNA Microarray Technology

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  • Fumiaki Sato
  • Soken Tsuchiya
  • Kazuya Terasawa
  • Gozoh Tsujimoto

Abstract

Over the last decade, DNA microarray technology has provided a great contribution to the life sciences. The MicroArray Quality Control (MAQC) project demonstrated the way to analyze the expression microarray. Recently, microarray technology has been utilized to analyze a comprehensive microRNA expression profiling. Currently, several platforms of microRNA microarray chips are commercially available. Thus, we compared repeatability and comparability of five different microRNA microarray platforms (Agilent, Ambion, Exiqon, Invitrogen and Toray) using 309 microRNAs probes, and the Taqman microRNA system using 142 microRNA probes. This study demonstrated that microRNA microarray has high intra-platform repeatability and comparability to quantitative RT-PCR of microRNA. Among the five platforms, Agilent and Toray array showed relatively better performances than the others. However, the current lineup of commercially available microRNA microarray systems fails to show good inter-platform concordance, probably because of lack of an adequate normalization method and severe divergence in stringency of detection call criteria between different platforms. This study provided the basic information about the performance and the problems specific to the current microRNA microarray systems.

Suggested Citation

  • Fumiaki Sato & Soken Tsuchiya & Kazuya Terasawa & Gozoh Tsujimoto, 2009. "Intra-Platform Repeatability and Inter-Platform Comparability of MicroRNA Microarray Technology," PLOS ONE, Public Library of Science, vol. 4(5), pages 1-12, May.
    • Handle: RePEc:plo:pone00:0005540
    DOI: 10.1371/journal.pone.0005540
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    1. Agnė Šatrauskienė & Rokas Navickas & Aleksandras Laucevičius & Tomas Krilavičius & Rūta Užupytė & Monika Zdanytė & Ligita Ryliškytė & Agnė Jucevičienė & Paul Holvoet, 2021. "Mir-1, miR-122, miR-132, and miR-133 Are Related to Subclinical Aortic Atherosclerosis Associated with Metabolic Syndrome," IJERPH, MDPI, vol. 18(4), pages 1-14, February.
    2. Swanhild U Meyer & Sebastian Kaiser & Carola Wagner & Christian Thirion & Michael W Pfaffl, 2012. "Profound Effect of Profiling Platform and Normalization Strategy on Detection of Differentially Expressed MicroRNAs – A Comparative Study," PLOS ONE, Public Library of Science, vol. 7(6), pages 1-13, June.
    3. Bin Wang & Paul Howel & Skjalg Bruheim & Jingfang Ju & Laurie B Owen & Oystein Fodstad & Yaguang Xi, 2011. "Systematic Evaluation of Three microRNA Profiling Platforms: Microarray, Beads Array, and Quantitative Real-Time PCR Array," PLOS ONE, Public Library of Science, vol. 6(2), pages 1-12, February.
    4. Jin-Xing Liu & Yong Xu & Chun-Hou Zheng & Yi Wang & Jing-Yu Yang, 2012. "Characteristic Gene Selection via Weighting Principal Components by Singular Values," PLOS ONE, Public Library of Science, vol. 7(7), pages 1-10, July.

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