Microarrays vs Quantitative PCR for Measuring miRNAs

Two common methods for measuring miRNAs in a total RNA sample are microarrays and quantitative RT-PCR (qPCR). To understand the results of studies that use these two different techniques to measure miRNAs, it is important to understand how well the results of these two analysis methods correlate. Since both methods use total RNA as a starting material, it is also critical to understand how measurement of miRNAs might be affected by the particular method of total RNA preparation used.

A study involved measurement of the expression of 470 human miRNAs in nine human tissues using Agilent microarrays, and comparison of these results to qPCR profiles of 61 miRNAs in the same tissues (Ach et al. 2008). Most expressed miRNAs (53/60) correlated well between the two methods. Using spiked-in synthetic miRNAs, the two miRNAs with the lowest correlations were further examined, and the differences found could not be attributed to differential sensitivity of the two methods. Three widely-used total RNA sample prep methods using miRNA microarrays were also tested. Although almost all miRNA levels corresponded between the three methods, there were a few miRNAs whose levels consistently differed between the different prep techniques when measured by microarray analysis. These differences were corroborated by qPCR measurements.

The correlations between results of Agilent miRNA microarray and qPCR are generally excellent, as are the correlations between different total RNA prep methods. However, there are a few miRNAs whose levels do not correlate between the microarray and qPCR measurements, or between different sample prep methods. This should be considered when comparing results obtained using different analysis or sample preparation methods.

Point-of-Care Detection of Circulating miRNAs as Biomarkers

Originally identified as intracellular modulators of protein synthesis via posttranscriptional gene silencing, miRNAs were found to travel in extracellular human fluids (circulating miRNAs) inside specialized vesicles known as exosomes. Their content inside exosomes changes during pathological events. There are >100 circulating miRNAs that can be used as biomarkers. A portable microarray POC device combining PCR and microarray platform is useful for the detection of circulating miRNAs (Vaca 2014). It reduces time for sample preparation and has enough sensitivity to detect a handful of molecules in the plasma. It is not only an auxiliary tool in diagnosis, but also useful for determining sensitivity of a patient to a particular drug in personalized medicine.

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