Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression
- 1 April 2010
- journal article
- research article
- Published by Cold Spring Harbor Laboratory in RNA
- Vol. 16 (5), 991-1006
- https://doi.org/10.1261/rna.1947110
Abstract
RNA abundance and DNA copy number are routinely measured in high-throughput using microarray and next-generation sequencing (NGS) technologies, and the attributes of different platforms have been extensively analyzed. Recently, the application of both microarrays and NGS has expanded to include microRNAs (miRNAs), but the relative performance of these methods has not been rigorously characterized. We analyzed three biological samples across six miRNA microarray platforms and compared their hybridization performance. We examined the utility of these platforms, as well as NGS, for the detection of differentially expressed miRNAs. We then validated the results for 89 miRNAs by real-time RT-PCR and challenged the use of this assay as a “gold standard.” Finally, we implemented a novel method to evaluate false-positive and false-negative rates for all methods in the absence of a reference method.Keywords
This publication has 47 references indexed in Scilit:
- miR2Disease: a manually curated database for microRNA deregulation in human diseaseNucleic Acids Research, 2009
- RISC-target interaction: Cleavage and translational suppressionBiochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2008
- Highly sensitive and specific microRNA expression profiling using BeadArray technologyNucleic Acids Research, 2008
- Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targetsGenome Research, 2008
- Profiling microRNA expression with microarraysTrends in Biotechnology, 2008
- Identification of microRNAs and other small regulatory RNAs using cDNA library sequencingMethods, 2008
- miRBase: tools for microRNA genomicsNucleic Acids Research, 2007
- A Mammalian microRNA Expression Atlas Based on Small RNA Library SequencingCell, 2007
- miRGen: a database for the study of animal microRNA genomic organization and functionNucleic Acids Research, 2006
- The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurementsNature Biotechnology, 2006