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

(2014) NATURE METHODS. 11(8). p.809-815
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Bioinformatics: from nucleotids to networks (N2N)
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 micro RNA 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.
Keywords
CONCORDANCE

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Citation

Please use this url to cite or link to this publication:

Chicago
Mestdagh, Pieter, Nicole Hartmann, Lukas Baeriswy, Ditte Andreasen, Nathalie Bernard, Caifu Chen, David Cheo, et al. 2014. “Evaluation of Quantitative miRNA Expression Platforms in the microRNA Quality Control (miRQC) Study.” Nature Methods 11 (8): 809–815.
APA
Mestdagh, P., Hartmann, N., Baeriswy, L., Andreasen, D., Bernard, N., Chen, C., Cheo, D., et al. (2014). Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study. NATURE METHODS, 11(8), 809–815.
Vancouver
1.
Mestdagh P, Hartmann N, Baeriswy L, Andreasen D, Bernard N, Chen C, et al. Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study. NATURE METHODS. 2014;11(8):809–15.
MLA
Mestdagh, Pieter, Nicole Hartmann, Lukas Baeriswy, et al. “Evaluation of Quantitative miRNA Expression Platforms in the microRNA Quality Control (miRQC) Study.” NATURE METHODS 11.8 (2014): 809–815. Print.
@article{6844192,
  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 micro RNA 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.},
  author       = {Mestdagh, Pieter and Hartmann, Nicole and Baeriswy, Lukas and Andreasen, Ditte and Bernard, Nathalie and Chen, Caifu and Cheo, David and D'Andrade, Petula and DeMayo, Mike and Dennis, Lucas and Derveaux, Stefaan and Feng, Yun and Fulmer-Smentek, Stephanie and Gerstmayer, Bernhard and Gouffon, Julia and Grimley, Chris and Lader, Eric and Lee, Kathy Y and Luo, Shujun and Mouritzen, Peter and Narayanan, Aishwarya and Patel, Sunali and Peiffer, Sabine and Ruberg, Silvia and Schroth, Gary and Schuster, Dave and Shaffer, Jonathan M and Shelton, Elliot J and Silveria, Scott and Ulmanella, Umberto and Veeramachaneni, Vamsi and Staedtler, Frank and Peters, Thomas and Guettouche, Toumy and Wong, Linda and Vandesompele, Jo},
  issn         = {1548-7091},
  journal      = {NATURE METHODS},
  keyword      = {CONCORDANCE},
  language     = {eng},
  number       = {8},
  pages        = {809--815},
  title        = {Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study},
  url          = {http://dx.doi.org/10.1038/NMETH.3014},
  volume       = {11},
  year         = {2014},
}

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