6 research outputs found
Multi-Platform Analysis of MicroRNA Expression Measurements in RNA from Fresh Frozen and FFPE Tissues
<div><p>MicroRNAs play a role in regulating diverse biological processes and have considerable utility as molecular markers for diagnosis and monitoring of human disease. Several technologies are available commercially for measuring microRNA expression. However, cross-platform comparisons do not necessarily correlate well, making it difficult to determine which platform most closely represents the true microRNA expression level in a tissue. To address this issue, we have analyzed RNA derived from cell lines, as well as fresh frozen and formalin-fixed paraffin embedded tissues, using Affymetrix, Agilent, and Illumina microRNA arrays, NanoString counting, and Illumina Next Generation Sequencing. We compared the performance within- and between the different platforms, and then verified these results with those of quantitative PCR data. Our results demonstrate that the within-platform reproducibility for each method is consistently high and although the gene expression profiles from each platform show unique traits, comparison of genes that were commonly detectable showed that detection of microRNA transcripts was similar across multiple platforms.</p> </div
Replicate performance of tested miRNA platforms.
*<p>The miRNA transcripts interrogated by each platform were assessed based on platform-specific metrics. n =  number of interrogated transcripts by each platform and were used to calculate the Pearson Correlations(r).</p
Experimental design of the miRNA expression platform comparison.
<p>RNA from replicate samples derived from normal lung, lung tumor, and a cell line were extracted by methods as indicated. All samples were subsequently analyzed by Illumina, Affymetrix, Agilent, NanoString, Illumina miRNA-Seq, and Fluidigm qPCR.</p
Expression correlations of data derived from fresh frozen (FF) and paraffin-embedded (FFPE) samples.
<p>Correlations of log2 transformed signal counts for each platform are shown (A–F) along with the respective Pearson correlation (r) coefficients. The average expression values of two replicates were used except for miRNA-Seq, where individual samples were directly compared as indicated.</p
Fractional deviation from the mean miRNA expression for the top ranked 100 miRNA transcripts.
<p>For each sample (A–F), the fractional deviation was plotted by each platform against the mean scaled expression of the ranked miRNA transcripts.</p
Correlation of miRNA expression fold-change in Fluidigm-based qPCR compared to five other miRNA gene profiling platforms.
*<p>The number of miRNA transcripts shared among all platforms and detected by qPCR in the fresh frozen and formalin-fixed paraffin embedded samples as indicated. Spearman correlation coefficient (r<sub>s</sub>) and its associated p-value are indicated.</p