MicroRNAs are important negative regulators of protein-coding gene expression and have been studied intensively over the past years. Several measurement platforms have been developed to determine relative miRNA abundance in biological samples using different technologies such as small RNA sequencing, reverse transcription–quantitative PCR (RT-qPCR) and (microarray) hybridization. In this study, we systematically compared 12 commercially available platforms for analysis of microRNA expression. We measured an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples and synthetic spikes from microRNA family members with varying homology. We developed robust quality metrics to objectively assess platform performance in terms of reproducibility, sensitivity, accuracy, specificity and concordance of differential expression. The results indicate that each method has its strengths and weaknesses, which help to guide informed selection of a quantitative microRNA gene expression platform for particular study goals.
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We thank J. Nuytens for preparing all RNA samples and E. Lefebvre and T. Demoor for statistical and mathematical support. P. Mestdagh is supported by the Fund for Scientific Research Flanders (FWO); J.V. is supported by the Ghent University Research Fund (BOF).
D.A. and P. Mouritzen are employed by Exiqon; N.B., C.C., K.L., S.P atel., E.S. and U.U. are employed by Life Technologies; D.C., Y.F. and D.S. are employed by Quanta Biosciences; P.D. and S.F. are employed by Agilent Technologies; M.D. and J.G. are employed by Affymetrix; L.D. and C.G. are employed by NanoString Technologies; S.D. and S.S. are employed by WaferGen; E.L. and J.S. are employed by Qiagen; S.L. and G.S. are employed by Illumina. MiRNA profiling experiments were performed at the expense of Exiqon, Life Technologies, Agilent Technologies, Quanta Biosciences, Qiagen, WaferGen, Illumina and NanoString Technologies.
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Mestdagh, P., Hartmann, N., Baeriswyl, L. et al. Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study. Nat Methods 11, 809–815 (2014). https://doi.org/10.1038/nmeth.3014
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