使用外源 RNA 内参 Spike-in 控制混合物评估差异基因表达实验中的技术性能。

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures.

机构信息

1] National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, USA [2] Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, California 94305, USA.

National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, USA.

出版信息

Nat Commun. 2014 Sep 25;5:5125. doi: 10.1038/ncomms6125.

DOI:10.1038/ncomms6125

PMID:25254650

Abstract

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.

摘要

对于评估、报告和比较基因组规模差异基因表达实验的技术性能，需要采用标准方法。在这里，我们使用源自外部 Spike-in RNA 对照比率混合物分析得出的标准“仪表板”来评估技术性能。这些具有定义丰度比的对照比率混合物可用于评估差异表达转录本列表的诊断性能、比率（LODR）估计值和表达比率变异性以及测量偏差的检测限。性能指标套件适用于典型实验的分析，在这里我们还应用这些指标来评估不同实验室之间的技术性能。一项使用在 12 个实验室之间共享的相同样本的实验室间研究，使用三种不同的测量过程，证明了在 11 个实验室中普遍具有一致的诊断能力。对于相同的测量过程，实验室之间的比率测量变异性和偏差也具有可比性。我们观察到使用不同的 mRNA 富集方案的测量过程存在不同的偏差。