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Table 3 miRNA quantification technology

From: Methods and novel technology for microRNA quantification in colorectal cancer screening

Technology Advantages Limitations Citations
qPCR • Current gold standard for sensitivity and specificity • No genome-wide coverage [74,75,76]
Microarray • Commercially available reagents
• Genome-wide coverage
• Specific probes
• Specialized equipment
• Lack of reproducibility between platforms
• Difficult data normalization
[81,82,83,84,85,86,87]
NGS • Genome-wide coverage
• Multiple samples may be run in parallel
• Promotes novel miRNA discovery
• Can detect polymorphisms
• Complicated, non-standardized data analysis [93,94,95,96,97]
Isothermal amplification • No need for thermocycling equipment
• Can improve existing qPCR, microarray, and NGS methods
• Disadvantages are technique-specific (see below) [101]
 • Exponential amplification • High sensitivity • May require a nicking enzyme, which complicates primer design [102, 103]
 • Rolling circle amplification • 1 primer
• Can be optimized for linear or exponential amplification
• Requires 2 enzymes (polymerase and ligase)
• Initial denaturation not performed at room temperature
[105,106,107,108,109]
 • Duplex-specific nuclease signal amplification • High specificity • Enzyme is not readily available [110,111,112,113]
 • Hybridization chain reaction • No polymerase • Linear amplification only [114,115,116,117,118,119,120]
Near-infrared technology • No autofluoresence
• Minimal photobleaching
• No tedious treatment of sample before or after the test
• Lanthanide probes are not yet commercially available and must be optimized [132, 140,141,142,143]