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

Wang B, Howel P, Bruheim S, Ju J, Owen LB, Fodstad O, Xi Y - PLoS ONE (2011)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Mathematics and Statistics, University of South Alabama College of Arts and Sciences, Mobile, Alabama, United States of America.

ABSTRACT

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.

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Related in: MedlinePlus

Stability evaluation for endogenous controls/probes from three platforms.The box plots of coefficient of variation (CV) values for each projected normalizer are calculated by using the measures of the replicates. Ctrl, Cis, Dox, and Ifo represent control, and three different chemo drug treatments.
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pone-0017167-g005: Stability evaluation for endogenous controls/probes from three platforms.The box plots of coefficient of variation (CV) values for each projected normalizer are calculated by using the measures of the replicates. Ctrl, Cis, Dox, and Ifo represent control, and three different chemo drug treatments.

Mentions: To compare the stability of all endogenous controls/probes used within the three platforms, we again employed CVs by taking the expression levels into consideration (Figure 5). For the TLDA and LNA arrays, the CVs were computed based on the replicates of each control/probe in a single array, while in the beads array, the CVs were computed based on the intensities after intra-sample normalization for the four normalization beads from the five pools for each sample. From Figure 5, we find that the CVs of the four snoRNAs in LNA array have much larger means and variances compared to those on the other two platforms. Three endogenous controls in TLDA have the best performance with the small means and standard deviations.


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

Wang B, Howel P, Bruheim S, Ju J, Owen LB, Fodstad O, Xi Y - PLoS ONE (2011)

Stability evaluation for endogenous controls/probes from three platforms.The box plots of coefficient of variation (CV) values for each projected normalizer are calculated by using the measures of the replicates. Ctrl, Cis, Dox, and Ifo represent control, and three different chemo drug treatments.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3037970&req=5

pone-0017167-g005: Stability evaluation for endogenous controls/probes from three platforms.The box plots of coefficient of variation (CV) values for each projected normalizer are calculated by using the measures of the replicates. Ctrl, Cis, Dox, and Ifo represent control, and three different chemo drug treatments.
Mentions: To compare the stability of all endogenous controls/probes used within the three platforms, we again employed CVs by taking the expression levels into consideration (Figure 5). For the TLDA and LNA arrays, the CVs were computed based on the replicates of each control/probe in a single array, while in the beads array, the CVs were computed based on the intensities after intra-sample normalization for the four normalization beads from the five pools for each sample. From Figure 5, we find that the CVs of the four snoRNAs in LNA array have much larger means and variances compared to those on the other two platforms. Three endogenous controls in TLDA have the best performance with the small means and standard deviations.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Mathematics and Statistics, University of South Alabama College of Arts and Sciences, Mobile, Alabama, United States of America.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus