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Detection of human microRNAs across miRNA Array and Next Generation DNA Sequencing Platforms
Citation:
HESTER, S. D., C. Harrington, H. Auer, W. Wang, S. Potter, D. Baldwin, J. Tiesman, N. Jafari, N. DENSLOW, P. A. Schweitzer, K. Dewar, J. Keileczawa, R. Steen, M. Zianni, S. Singh, A. Perera, D. Bintzler, AND M. M. Detwiler. Detection of human microRNAs across miRNA Array and Next Generation DNA Sequencing Platforms. Presented at 2009 Annual Meeting of ABRF, Nashville, TN, February 09 - 12, 2009.
Impact/Purpose:
Evaluates performance of microRNA arrays compared to Ultra-highthrough sequencing. This study serves as a n=benchmark for selecting microRNA platforms.
Description:
microRNA (miRNAs) are non-coding RNA molecules between 19 and 30 nucleotides in length that are believed to regulate approximately 30 per cent of all human genes. They act as negative regulators of their gene targets in many biological processes. Recent developments in microarray options and the introduction of high throughput DNA sequencing technologies now make it possible to use these advanced platforms for miRNA-expression profiling. To determine the effectiveness of each of these platforms in measuring miRNA expression and to compare the accuracy of the profiles generated with each platform with quantitiative RT-PCR analysis, the Microarray Research Group (MARG) and the DNA Sequencing Group (DSRG) developed a joint research project. The goal of the MARG component of the research project is to evaluate miRNA platforms for their ability to detect miRNAs from complex total RNA samples. In addition to 3 DNA microarray platforms, two PCR-based platforms are included in the study for performance comparison. Each of the 5 miRNA platforms will be tested with total RNAs to evaluate the ability of each platform to detect and measure individual miRNAs in a complex biological sample. Aliquots from single pools of two human tissue RNAs from the Ambion mirVANA Reference Panel will be analyzed at separate test sites for each of the following miRNA platforms: Agilent miRNA microarray, Illumina miRNA expression panel, Exiqon miRCURY LNA arrays, Applied Biosystems TaqMan miRNA assay, and FlexmiR by Luminex. The second component of the study will be conducted in collaboration with the DSRG. miRNA expression profiles of the total RNAs used in the microarray phase of this study will be determined using “Next Generation” high throughput (HT) DNA sequencer, Solexa,. The miRNA profiles produced by the HT DNA sequencer will be compared to the miRNA array platform results to determine correspondence of the two technologies, with a common reference to RT-PCR data.