Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures
Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures
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DOI：
10.1038/ncomms6125
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发表时间：
2014-09-01
影响因子：
16.6
通讯作者：
Salit, Marc
中科院分区：
文献类型：
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作者：
Munro, Sarah A.;Lund, Steven P.;Salit, Marc
迫切需要标准的方法来评估、报告和比较基因组规模差异基因表达实验的技术性能。在这里，我们使用一个拟议的标准“仪表板”来评估技术性能，该标准是从外部尖峰RNA控制率混合物的分析中得出的。这些具有定义丰度比的对照比率混合物能够评估差异表达转录本列表的诊断性能、比率的检测极限(LODR)估计以及表达比率的变异性和测量偏差。性能指标套件适用于典型实验的分析，这里我们也应用这些指标来评估实验室之间的技术性能。一项实验室间研究使用了具有三种不同测量过程的12个实验室共享的相同样本，表明11个实验室的诊断能力大体一致。对于相同的测量过程，不同实验室之间的比率、测量变异性和偏差也具有可比性。我们使用不同的信使核糖核酸富集法观察到测量过程的不同偏差。
There is a critical need for standard approaches to assess, report and compare the technical performance of genome-scale differential gene expression experiments. Here we assess technical performance with a proposed standard 'dashboard' of metrics derived from analysis of external spike-in RNA control ratio mixtures. These control ratio mixtures with defined abundance ratios enable assessment of diagnostic performance of differentially expressed transcript lists, limit of detection of ratio (LODR) estimates and expression ratio variability and measurement bias. The performance metrics suite is applicable to analysis of a typical experiment, and here we also apply these metrics to evaluate technical performance among laboratories. An interlaboratory study using identical samples shared among 12 laboratories with three different measurement processes demonstrates generally consistent diagnostic power across 11 laboratories. Ratio measurement variability and bias are also comparable among laboratories for the same measurement process. We observe different biases for measurement processes using different mRNA-enrichment protocols.