Nature Biotechnology
- 24, 1115 - 1122 (2006)
Published online: 8 September 2006; | doi:10.1038/nbt1236
Evaluation of DNA microarray results with quantitative gene expression platformsRoger D Canales1, 10, Yuling Luo2, 10, James C Willey3, 10, Bradley Austermiller3, Catalin C Barbacioru1, Cecilie Boysen4, Kathryn Hunkapiller1, Roderick V Jensen5, Charles R Knight6, Kathleen Y Lee1, Yunqing Ma2, Botoul Maqsodi2, Adam Papallo5, Elizabeth Herness Peters6, Karen Poulter1, Patricia L Ruppel7, Raymond R Samaha1, Leming Shi8, Wen Yang2, Lu Zhang1 & Federico M Goodsaid91
Applied Biosystems, 850 Lincoln Centre Dr., Foster City, California 94404, USA. 2
Panomics, Inc., 6519 Dumbarton Circle, Fremont, California 94555, USA. 3
University of Toledo, Toledo, Ohio 43614, USA. 4
ViaLogy Corp., 2400 Lincoln Avenue, Altadena, California 91001, USA. 5
University of Massachusetts-Boston, 100 Morrissey Blvd., Boston, Massachusetts 02125, USA. 6
Gene Express, Inc., 975 Research Drive, Toledo, Ohio 43614, USA. 7
Innovative Analytics, 7107 Elm Valley Dr., Kalamazoo, Michigan 49009, USA. 8
National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, Arkansas 72079, USA. 9
Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Ave., Silver Spring, Maryland 20993, USA. 10
These authors contributed equally to this work.
Correspondence should be addressed to Federico M Goodsaid Federico.Goodsaid@fda.hhs.gov 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.
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