Learning from microarray interlaboratory studies: measures of precision for gene expression
Learning from microarray interlaboratory studies: measures of precision for gene expression
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DOI：
10.1186/1471-2164-10-153
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发表时间：
2009-04-08
期刊：
影响因子：
4.4
通讯作者：
Salit, Marc
中科院分区：
文献类型：
--
作者：
Duewer, David L.;Jones, Wendell D.;Salit, Marc
背景资料：证明基因表达微阵列结果的可重复性的能力是微阵列技术在临床应用中使用的关键考虑因素。虽然研究已经断言微阵列数据在给定条件下可以是“高度可再现的”，但是在用于表征和表达测量性能的各种度量和术语之间进行定量比较的能力很小。使用标准化的概念工具可以极大地促进微阵列社区的用户、开发者和监管者利益相关者之间的沟通。虽然受到高度复用系统的影响，（计量学）致力于建立一个连贯的和国际公认的词汇和定量的做法来表征测量process.Results：两个独立的方面的测量概念的“准确度”是“真实度”（接近的测量到一个公认的参考值）和“精度”（接近的测量结果彼此）。一个精心设计的合作研究，使各种基因表达测量精度指标的估计：重复性，中间精密度和再现性的几种口味。三个2004年的表达分析试点能力测试合作研究，每个有13至16名参与者，提供了两个参考RNA池的每一个三份微阵列测量。我们使用并适度扩展了一致的ISO 5725文件标准，评估了单个微阵列信号测量的最佳精密度品质因数，从适合单个测量过程的计算（例如微阵列上单个探针的技术重复表达值），到代表给定平台中所有探针的精密度函数的估计和显示。只有适度的扩展，所建立的并行框架可以卓有成效地用于表征微阵列和其他高度复用系统的测量性能。精密度函数，总结常规精密度指标估计从适当的重复测量的一个或多个参考材料作为信号电平的函数，证明和值得进一步发展的特点测量平台，监测测量系统性能的变化，并比较实验室或分析师之间的性能。
Background: The ability to demonstrate the reproducibility of gene expression microarray results is a critical consideration for the use of microarray technology in clinical applications. While studies have asserted that microarray data can be "highly reproducible" under given conditions, there is little ability to quantitatively compare amongst the various metrics and terminology used to characterize and express measurement performance. Use of standardized conceptual tools can greatly facilitate communication among the user, developer, and regulator stakeholders of the microarray community. While shaped by less highly multiplexed systems, measurement science (metrology) is devoted to establishing a coherent and internationally recognized vocabulary and quantitative practice for the characterization of measurement processes.Results: The two independent aspects of the metrological concept of "accuracy" are "trueness" (closeness of a measurement to an accepted reference value) and "precision" (the closeness of measurement results to each other). A carefully designed collaborative study enables estimation of a variety of gene expression measurement precision metrics: repeatability, several flavors of intermediate precision, and reproducibility. The three 2004 Expression Analysis Pilot Proficiency Test collaborative studies, each with 13 to 16 participants, provide triplicate microarray measurements on each of two reference RNA pools. Using and modestly extending the consensus ISO 5725 documentary standard, we evaluate the metrological precision figures of merit for individual microarray signal measurement, building from calculations appropriate to single measurement processes, such as technical replicate expression values for individual probes on a microarray, to the estimation and display of precision functions representing all of the probes in a given platform.Conclusion: With only modest extensions, the established metrological framework can be fruitfully used to characterize the measurement performance of microarray and other highly multiplexed systems. Precision functions, summarizing routine precision metrics estimated from appropriately repeated measurements of one or more reference materials as functions of signal level, are demonstrated and merit further development for characterizing measurement platforms, monitoring changes in measurement system performance, and comparing performance among laboratories or analysts.