Evaluation of DNA microarray results with quantitative gene expression platforms.
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.
Canales
Roger D
RD
Applied Biosystems, 850 Lincoln Centre Dr., Foster City, California 94404, USA.
Luo
Yuling
Y
Willey
James C
JC
Austermiller
Bradley
B
Barbacioru
Catalin C
CC
Boysen
Cecilie
C
Hunkapiller
Kathryn
K
Jensen
Roderick V
RV
Knight
Charles R
CR
Lee
Kathleen Y
KY
Ma
Yunqing
Y
Maqsodi
Botoul
B
Papallo
Adam
A
Peters
Elizabeth Herness
EH
Poulter
Karen
K
Ruppel
Patricia L
PL
Samaha
Raymond R
RR
Shi
Leming
L
Yang
Wen
W
Zhang
Lu
L
Goodsaid
Federico M
FM
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