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Cited by 619

Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study

Mestdagh, Pieter, Hartmann, Nicole, Baeriswyl, Lukas, Andreasen, Ditte, Bernard, Nathalie, Chen, Caifu, Cheo, David, D'Andrade, Petula +28 more·2014·Nature Methods
DOI 10.1038/nmeth.3014
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Abstract

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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Crossref · 10.1038/nmeth.3014

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  • Methods that fail to acquire isomiRs significantly underestimate the presence of microRNAs in a variable fashion.

    “suggesting methods that fail to acquire isomiRs significantly underestimate the presence of microRNAs in a variable fashion (Mestdagh et al. 2014).”

    From Toward the human cellular microRNAome (2017) · cites this paper as Mestdagh et al. 2014

  • This could explain some of the variability of microRNA expression across methods demonstrated by the miRQC project.

    “This could explain some of the variability of microRNA expression across methods demonstrated by the miRQC project (particularly between RNA-seq and hybridization approaches) (Mestdagh et al. 2014) and impact the biologic activity of mimics and inhibitors relative to the true microRNA 5p end (Guo et al. 2014).”

    From Toward the human cellular microRNAome (2017) · cites this paper as Mestdagh et al. 2014

  • This was quite variable and rarely >90%.

    “This was quite variable and rarely >90%, suggesting methods that fail to acquire isomiRs significantly underestimate the presence of microRNAs in a variable fashion (Mestdagh et al. 2014).”

    From Toward the human cellular microRNAome (2017) · cites this paper as Mestdagh et al. 2014

  • The data clearly demonstrate a need to revise our understanding of the appropriate canonical microRNA sequences for better reproducibility and computational target prediction.

    “Although technical factors may be responsible for some variation between cell types, the data clearly demonstrate a need to revise our understanding of the appropriate canonical microRNA sequences for better reproducibility and computational target prediction (Mestdagh et al. 2014; Agarwal et al. 2015).”

    From Toward the human cellular microRNAome (2017) · cites this paper as Mestdagh et al. 2014

  • The microarray platform shows high reproducibility as evidenced by the miRQC study (5).

    “We used a microarray platform for miRNA expression detection since this platform shows a high reproducibility as evidenced by the miRQC study (5).”

    From Distribution of miRNA expression across human tissues (2016) · cites this paper as [5]

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Authors
Mestdagh, P., Hartmann, N., Baeriswyl, L., Andreasen, D., Bernard, N., Chen, C., Cheo, D., D'Andrade, P., DeMayo, M., Dennis, L., Derveaux, S., Feng, Y., Fulmer-Smentek, S., Gerstmayer, B., Gouffon, J., Grimley, C., Lader, E., Lee, K. Y., Luo, S., Mouritzen, P., Narayanan, A., Patel, S., Peiffer, S., Rüberg, S., Schroth, G., Schuster, D., Shaffer, J. M., Shelton, E. J., Silveria, S., Ulmanella, U., Veeramachaneni, V., Staedtler, F., Peters, T., Guettouche, T., Wong, L., & Vandesompele, J.
ORCID
Venue
Nature Methods
Publisher
Springer Science and Business Media LLC
Published
2014-06-29
Volume
11
Issue
8
Pages
809-815
ISSN
  • 1548-7091
  • 1548-7105
DOI
10.1038/nmeth.3014
Cited by
619
References
1
Language
en
Update notices
erratum (2014-08-28)
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