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

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.

[1]  Leming Shi,et al.  Using RNA sample titrations to assess microarray platform performance and normalization techniques , 2006, Nature Biotechnology.

[2]  Maqc Consortium.  The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements , 2006, Nature Biotechnology.

[3]  Brian S. Roberts,et al.  Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs. , 2005, RNA.

[4]  Stephen C. Harris,et al.  Rat toxicogenomic study reveals analytical consistency across microarray platforms , 2006, Nature Biotechnology.

[5]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[6]  Phillip D. Zamore,et al.  Ribo-gnome: The Big World of Small RNAs , 2005, Science.

[7]  Jin-Wu Nam,et al.  Genomics of microRNA. , 2006, Trends in genetics : TIG.

[8]  Sam Griffiths-Jones,et al.  The microRNA Registry , 2004, Nucleic Acids Res..

[9]  Anton J. Enright,et al.  Human MicroRNA Targets , 2004, PLoS biology.

[10]  Catalin C. Barbacioru,et al.  Evaluation of DNA microarray results with quantitative gene expression platforms , 2006, Nature Biotechnology.

[11]  H. Horvitz,et al.  MicroRNA expression profiles classify human cancers , 2005, Nature.

[12]  R. Carthew,et al.  Expanding roles for miRNAs and siRNAs in cell regulation. , 2004, Current opinion in cell biology.

[13]  Yu Liang,et al.  BMC Genomics , 2007 .

[14]  P. Collins,et al.  Performance comparison of one-color and two-color platforms within the Microarray Quality Control (MAQC) project , 2006, Nature Biotechnology.

[15]  C. Sander,et al.  A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing , 2007, Cell.

[16]  J. Shendure.  The beginning of the end for microarrays? , 2008, Nature Methods.

[17]  T. Tuschl,et al.  Identification of Novel Genes Coding for Small Expressed RNAs , 2001, Science.

[18]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[19]  Weida Tong,et al.  Evaluation of external RNA controls for the assessment of microarray performance , 2006, Nature Biotechnology.

[20]  Stijn van Dongen,et al.  miRBase: microRNA sequences, targets and gene nomenclature , 2005, Nucleic Acids Res..

[21]  M. Rosbash,et al.  Three abundance classes in HeLa cell messenger RNA , 1974, Nature.