Journal Article

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

Guettouche, Toumy, Grimley, Chris, Mouritzen, Peter, Peiffer, Sabine, Shaffer, Jonathan M, Staedtler, Frank, Lee, Kathy Y, Fulmer-Smentek, Stephanie, Schuster, Dave, Luo, Shujun, Shelton, Elliot J, Bernard, Nathalie, Ulmanella, Umberto, Derveaux, Stefaan, DeMayo, Mike, Feng, Yun, Schroth, Gary, Andreasen, Ditte, Veeramachaneni, Vamsi, Vandesompele, Jo, Silveria, Scott, D'Andrade, Petula, Chen, Caifu, Narayanan, Aishwarya, Patel, Sunali, Mestdagh, Pieter, Dennis, Lucas, Gouffon, Julia, Baeriswyl, Lukas, Peters, Thomas, Wong, Linda, Gerstmayer, Bernhard, Hartmann, Nicole, Rüberg, Silvia, Cheo, David, Lader, Eric

2014

Overview

12 microRNA expression profiling platforms are compared for their reproducibility, sensitivity, accuracy and specificity, and the strengths and weaknesses of each platform are discussed. 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.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 38 / 38/39 / 38/77 / 38/91 / 631/1647/2017 / 631/208/199 / 631/337/384/331 / analysis / Bioinformatics / Biological Microscopy / Biological samples / Biological Techniques / Biology / Biomedical Engineering/Biotechnology / Gene expression / Hybridization / Life Sciences / Methods / MicroRNA / MicroRNAs - genetics / Properties / Proteins / Proteomics / Quality Control / Reproducibility of Results / Ribonucleic acid / RNA / RNA sequencing