title: 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.
authors.affiliation: Applied Biosystems, 850 Lincoln Centre Dr., Foster City, California 94404, USA.
authors.forename: Roger D
authors.initials: RD
authors.lastname: Canales
authors.forename: Yuling
authors.initials: Y
authors.lastname: Luo
authors.forename: James C
authors.initials: JC
authors.lastname: Willey
authors.forename: Bradley
authors.initials: B
authors.lastname: Austermiller
authors.forename: Catalin C
authors.initials: CC
authors.lastname: Barbacioru
authors.forename: Cecilie
authors.initials: C
authors.lastname: Boysen
authors.forename: Kathryn
authors.initials: K
authors.lastname: Hunkapiller
authors.forename: Roderick V
authors.initials: RV
authors.lastname: Jensen
authors.forename: Charles R
authors.initials: CR
authors.lastname: Knight
authors.forename: Kathleen Y
authors.initials: KY
authors.lastname: Lee
authors.forename: Yunqing
authors.initials: Y
authors.lastname: Ma
authors.forename: Botoul
authors.initials: B
authors.lastname: Maqsodi
authors.forename: Adam
authors.initials: A
authors.lastname: Papallo
authors.forename: Elizabeth Herness
authors.initials: EH
authors.lastname: Peters
authors.forename: Karen
authors.initials: K
authors.lastname: Poulter
authors.forename: Patricia L
authors.initials: PL
authors.lastname: Ruppel
authors.forename: Raymond R
authors.initials: RR
authors.lastname: Samaha
authors.forename: Leming
authors.initials: L
authors.lastname: Shi
authors.forename: Wen
authors.initials: W
authors.lastname: Yang
authors.forename: Lu
authors.initials: L
authors.lastname: Zhang
authors.forename: Federico M
authors.initials: FM
authors.lastname: Goodsaid
mesh_terms: D004867:Equipment Design; D019544:Equipment Failure Analysis; D020869:Gene Expression Profiling / Q000295:instrumentation* / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods; D011785:Quality Assurance, Health Care / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity