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Performance evaluation of commercial miRNA expression array platforms

DOI: 10.1186/1756-0500-3-80

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Abstract:

We compared the performance characteristics of four commercial miRNA array technologies and found that all platforms performed well in separate measures of performance.The Ambion and Agilent platforms were more accurate, whereas the Illumina and Exiqon platforms were more specific. Furthermore, the data analysis approach had a large impact on the performance, predominantly by improving precision.MicroRNAs (miRNAs) are endogenous, non-coding transcripts that regulate a diverse range of functions, including development, differentiation, growth, apoptosis and metabolism. These 17-24 nucleotide RNA molecules confer specific recognition of target mRNAs and modulate gene expression by acting in conjunction with a set of effector proteins of the RNA interference pathway [1,2]. Through this interaction, miRNAs negatively regulate expression of specific target mRNAs by inhibiting translation, sequestering transcripts in P-bodies [3], or by accelerating mRNA decay as a consequence of rapid deadenylation[4]. Moreover, miRNAs have recently been proposed to activate translation of mRNAs under certain conditions [5].The relative abundance of miRNAs in cells is thought to be important for miRNAs to exert their regulatory function. For example, titrated expression of both genomic copies of mouse miR-1 is required for normal heart formation and function during embryogenesis [6]. Aberrant miRNA expression contributes to malignancies, tumor progression and metastasis (reviewed in [7]), and miRNA expression profiles can be correlated with disease pathogenesis and prognosis [8,9]. Thus, the performance characteristics of technologies that measure the relative abundance of miRNAs is important for effectively deciphering their functional roles and their potential utility as diagnostic biomarkers.Microarray technology permits simultaneous expression measurements for hundreds of miRNAs. This technology is already widely used and promises to become a standard tool in the near future. However

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