Evaluation of DNA microarray results with quantitative gene expression platforms

Abstract

We have evaluated the performance characteristics of three quantitative gene expression technologies and correlated their expression measurements to those of five commercial microarray platforms, based on the MicroArray Quality Control (MAQC) data set. The limit of detection, assay range, precision, accuracy and fold-change correlations were assessed for 997 TaqMan Gene Expression Assays, 205 Standardized RT (Sta)RT-PCR assays and 244 QuantiGene assays. TaqMan is a registered trademark of Roche Molecular Systems, Inc. We observed high correlation between quantitative gene expression values and microarray platform results and found few discordant measurements among all platforms. The main cause of variability was differences in probe sequence and thus target location. A second source of variability was the limited and variable sensitivity of the different microarray platforms for detecting weakly expressed genes, which affected interplatform and intersite reproducibility of differentially expressed genes. From this analysis, we conclude that the MAQC microarray data set has been validated by alternative quantitative gene expression platforms thus supporting the use of microarray platforms for the quantitative characterization of gene expression.

In vitro study of the effects of ELF electric fields on gene expression in human epidermal cells

“…It was demonstrated that data from the two different technologies, microarray and real-time rtPCR, yield comparable results [Canales et al, 2006;Morey et al, 2006]. In the present study, regulation of all tested up-regulated genes was confirmed.…”

Absolute quantification of microRNAs by using a universal reference

“…Due to the mRNA length, it is currently hardly possible to work with a fully synthetic mRNA standard as presented here for miRNAs. Therefore, although the different available microarray platforms for mRNA expression profiling have been extensively evaluated (Canales et al 2006), there is still no gold standard for quantifying mRNA transcript concentrations by microarrays. The approaches developed so far encompass mathematical modeling (Hekstra et al 2003;Frigessi et al 2005), calibrated reference samples (Dudley et al 2002), exogenous RNA controls (Carter et al 2005b), and combinations of mathematical modeling and spike measurements (Zhao et al 2007).…”

Custom Design of a GeXP Multiplexed Assay Used to Assess Expression Profiles of Inflammatory Gene Targets in Normal Colon, Polyp, and Tumor Tissue

“…Thus, slight differences in relative quantitation levels are not unexpected and studies have been conducted to assess differences in relative gene expression data obtained using different technology platforms. 5,31,32 Macroarray analysis relies on hybridization of labeled cDNA to probe regions on a nylon filter, whereas real-time PCR and GeXP assays involve PCR amplification procedures using primer assays. The preparation of labeled cDNA required for macroarray analysis thus is significantly different from production of reverse-transcribed cDNA for use as a template for PCR amplification.…”