miRNA Expression Profiling Using Illumina Universal BeadChips

We have developed a highly sensitive, specific, and reproducible method for microRNA (miRNA) expression profiling, using BeadArray technology. This method incorporates an enzyme-assisted specificity step, a solid-phase primer extension to distinguish between members of miRNA families. In addition, a universal PCR is used to amplify all targets prior to array hybridization. Using this method, highly reproducible miRNA expression profiles were generated with 100–200 ng total RNA input. The method has a 3.5–4 log (10⁵ –10⁹ molecules) dynamic range and is able to detect 1.2- to 1.3-fold differences between samples. Expression profiles generated by this method are highly comparable to those obtained with RT-PCR (R ² = 0.85–0.90) and direct sequencing (R = 0.87–0.89). This method should prove useful for high-throughput expression profiling of miRNAs in large numbers of tissue samples.