Evaluation of DNA microarray results with quantitative gene expression platforms
Evaluation of DNA microarray results with quantitative gene expression platforms
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DOI：
10.1038/nbt1236
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发表时间：
2006-09-01
影响因子：
46.9
通讯作者：
Goodsaid, Federico M.
中科院分区：
文献类型：
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作者：
Canales, Roger D.;Luo, Yuling;Goodsaid, Federico M.
我们已经评估了三种定量基因表达技术的性能特征，并将它们的表达测量与五种商业微阵列平台的表达测量相关联，基于微阵列质量控制（MAQC）数据集。评估了997个TaqMan基因表达测定、205个标准化RT（Sta）RT-PCR测定和244个QuantiGene测定的检测限、测定范围、精密度、准确度和倍数变化相关性。TaqMan是Roche Molecular Systems，Inc.的注册商标。我们观察到定量基因表达值和微阵列平台结果之间的高度相关性，并发现所有平台之间几乎没有不一致的测量结果。变异性的主要原因是探针序列的差异，因此是靶位置的差异。变异性的第二个来源是检测弱表达基因的不同微阵列平台的有限和可变灵敏度，这影响了差异表达基因的平台间和位点间重现性。从这个分析中，我们得出结论，MAQC微阵列数据集已通过替代的定量基因表达平台进行了验证，从而支持使用微阵列平台进行基因表达的定量表征。
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.