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Updated: May 16, 2026
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Probe-based Real-time PCR Approaches for Quantitative Measurement of microRNAs
Published on: April 14, 2015
Systematic evaluation of medium-throughput mRNA abundance platforms.
Stephenie D Prokopec1, John D Watson, Daryl M Waggott
1Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.
RNA (New York, N.Y.)
|November 22, 2012
Summary
This study compares NanoString nCounter and ABI OpenArray medium-throughput RNA quantification platforms against quantitative real-time RT-PCR. All platforms showed good concordance, but with different trade-offs in cost, time, and sensitivity.
Area of Science:
- Molecular biology
- Genomics
- Biotechnology
Background:
- High-throughput RNA profiling (microarrays, RNA-seq) is crucial but has systematic errors.
- Validation using alternate, medium-throughput technologies is standard practice for clinical and industrial applications.
- Medium-throughput platforms offer reproducibility, reduced sample input, and lower sensitivity to sample quality.
Purpose of the Study:
- To comprehensively compare two key medium-throughput RNA quantification platforms: NanoString's nCounter Analysis System and ABI's OpenArray System.
- To evaluate these platforms against the gold-standard quantitative real-time RT-PCR (RT-qPCR).
- To provide a benchmark for future evaluations of RNA quantification technologies.
Main Methods:
- Quantified 38 genes plus controls across 165 samples using NanoString nCounter, ABI OpenArray, and RT-qPCR.
- Compared signal:noise ratios, correlations, dynamic range, and detection accuracy between the platforms.
- Assessed trade-offs in price, time, and sensitivity for each technology.
Main Results:
- All three RNA quantification technologies demonstrated good concordance.
- Significant differences were observed in price, time efficiency, and sensitivity among the platforms.
- The study provides a detailed comparison of medium-throughput RNA quantification methods.
Conclusions:
- NanoString nCounter and ABI OpenArray are viable medium-throughput RNA quantification platforms with distinct advantages.
- The choice of platform depends on specific research needs regarding cost, speed, and sensitivity.
- This comparison offers a valuable dataset and framework for evaluating similar RNA quantification technologies.
