ArticleBMC genomics2009
Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 163 papers, 2 of them syntheses that pooled it.
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Who cites it
163 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- miRNAs as biomarkers for early cancer detection and their application in the development of new diagnostic tools.Biomedical engineering online · 2021Pooled it
- Systematic Review of Micro-RNA Expression in Pre-Eclampsia Identifies a Number of Common Pathways Associated with the Disease.PloS one · 2016Pooled it
- MicroRNA profiling in plasma samples using qPCR arrays: Recommendations for correct analysis and interpretation.PloS one · 2018Trial
- Plasma microRNA-451 as a novel hemolytic marker for β0-thalassemia/HbE disease.Molecular medicine reports · 2017Trial
- Plasma profile of microRNA after supplementation with high doses of vitamin D3 for 12 months.BMC research notes · 2012Trial
- Computational Method Using Attribute-Aware Message Passing and Graph Convolutional Network for Potential miRNA-Disease Association Prediction.International journal of molecular sciences · 2026Article
- Development of a rapid and simple Xeno Nucleic Acid (XNA) sensor-based microRNA detection platform for Parkinson's disease diagnostics.Journal of nanobiotechnology · 2026Article
- Epigenetic mechanisms and steroid-resistant nephrotic syndrome: The future potential for SRNS diagnosis.iScience · 2026Review
- Highly Sensitive Hybridization Chain Reaction-Based miRNA Detection Technology Using Diffusivity Analysis of Fluorescent Probe-Modified miRNA Particles.Sensors (Basel, Switzerland) · 2026Article
- Downregulation of miRNA-184 Promotes Nerve-Associated Angiogenesis via Vascular Endothelial Growth Factor A Following Ischemic Stroke.International journal of general medicine · 2026Article
- Ultra-Sensitive, Label-Free Detection of Nosocomial Infection RNA Biomarkers via CRISPR-Cas13a-Initiated PER-Driven DNA Walker.ACS omega · 2025Article
- Evaluation of Plasma microRNA-222 as a Biomarker for Gastric Cancer.Journal of clinical medicine · 2024Article
- MiRNA Expression in Long-Distance Runners with Musculoskeletal Pain: Implications for Pain Pathophysiology.Biomedicines · 2024Article
- Evaluation of genetic diversity within different rabbit (Archives animal breeding · 2024Article
- Selective miRNA quantitation with high-temperature thermal gel electrophoresis.Analytica chimica acta · 2023Article
- Circulating noncoding RNAs: promising biomarkers in liquid biopsy for the diagnosis, prognosis, and therapy of NSCLC.Discover oncology · 2023Review
- L1CAM immunocapture generates a unique extracellular vesicle population with a reproducible miRNA fingerprint.RNA biology · 2023Article
- Preparation and processing of dried blood spots for microRNA sequencing.Biology methods & protocols · 2023Review
- Circulating microRNAs as Reliable Tumor Biomarkers: Opportunities and Challenges Facing Clinical Application.The Journal of pharmacology and experimental therapeutics · 2023Review
- Article
103 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
backgroundMicroRNAs (miRNAs) have critical functions in various biological processes. MiRNA profiling is an important tool for the identification of differentially expressed miRNAs in normal cellular and disease processes. A technical challenge remains for high-throughput miRNA expression analysis as the number of miRNAs continues to increase with in silico prediction and experimental verification. Our study critically evaluated the performance of a novel miRNA expression profiling approach, quantitative RT-PCR array (qPCR-array), compared to miRNA detection with oligonucleotide microchip (microarray).
resultsHigh reproducibility with qPCR-array was demonstrated by comparing replicate results from the same RNA sample. Pre-amplification of the miRNA cDNA improved sensitivity of the qPCR-array and increased the number of detectable miRNAs. Furthermore, the relative expression levels of miRNAs were maintained after pre-amplification. When the performance of qPCR-array and microarrays were compared using different aliquots of the same RNA, a low correlation between the two methods (r=-0.443) indicated considerable variability between the two assay platforms. Higher variation between replicates was observed in miRNAs with low expression in both assays. Finally, a higher false positive rate of differential miRNA expression was observed using the microarray compared to the qPCR-array.
conclusionOur studies demonstrated high reproducibility of TaqMan qPCR-array. Comparison between different reverse transcription reactions and qPCR-arrays performed on different days indicated that reverse transcription reactions did not introduce significant variation in the results. The use of cDNA pre-amplification increased the sensitivity of miRNA detection. Although there was variability associated with pre-amplification in low abundance miRNAs, the latter did not involve any systemic bias in the estimation of miRNA expression. Comparison between microarray and qPCR-array indicated superior sensitivity and specificity of qPCR-array.
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