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Systematic evaluation of three microRNA profiling platforms: microarray, beads array, and quantitative real-time PCR array.

التفاصيل البيبلوغرافية
العنوان: Systematic evaluation of three microRNA profiling platforms: microarray, beads array, and quantitative real-time PCR array.
المؤلفون: Bin Wang, Paul Howel, Skjalg Bruheim, Jingfang Ju, Laurie B Owen, Oystein Fodstad, Yaguang Xi
المصدر: PLoS ONE, Vol 6, Iss 2, p e17167 (2011)
بيانات النشر: Public Library of Science (PLoS), 2011.
سنة النشر: 2011
المجموعة: LCC:Medicine
LCC:Science
مصطلحات موضوعية: Medicine, Science
الوصف: BACKGROUND: A number of gene-profiling methodologies have been applied to microRNA research. The diversity of the platforms and analytical methods makes the comparison and integration of cross-platform microRNA profiling data challenging. In this study, we systematically analyze three representative microRNA profiling platforms: Locked Nucleic Acid (LNA) microarray, beads array, and TaqMan quantitative real-time PCR Low Density Array (TLDA). METHODOLOGY/PRINCIPAL FINDINGS: The microRNA profiles of 40 human osteosarcoma xenograft samples were generated by LNA array, beads array, and TLDA. Results show that each of the three platforms perform similarly regarding intra-platform reproducibility or reproducibility of data within one platform while LNA array and TLDA had the best inter-platform reproducibility or reproducibility of data across platforms. The endogenous controls/probes contained in each platform have been observed for their stability under different treatments/environments; those included in TLDA have the best performance with minimal coefficients of variation. Importantly, we identify that the proper selection of normalization methods is critical for improving the inter-platform reproducibility, which is evidenced by the application of two non-linear normalization methods (loess and quantile) that substantially elevated the sensitivity and specificity of the statistical data assessment. CONCLUSIONS: Each platform is relatively stable in terms of its own microRNA profiling intra-reproducibility; however, the inter-platform reproducibility among different platforms is low. More microRNA specific normalization methods are in demand for cross-platform microRNA microarray data integration and comparison, which will improve the reproducibility and consistency between platforms.
نوع الوثيقة: article
وصف الملف: electronic resource
اللغة: English
تدمد: 1932-6203
Relation: http://europepmc.org/articles/PMC3037970?pdf=render; https://doaj.org/toc/1932-6203
DOI: 10.1371/journal.pone.0017167
URL الوصول: https://doaj.org/article/cf5c4edfd179409aac19802f19e3a91f
رقم الأكسشن: edsdoj.f5c4edfd179409aac19802f19e3a91f
قاعدة البيانات: Directory of Open Access Journals
الوصف
تدمد:19326203
DOI:10.1371/journal.pone.0017167