Duewer David L, Jones Wendell D, Reid Laura H, Salit Marc
Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8390, USA.
BMC Genomics. 2009 Apr 8;10:153. doi: 10.1186/1471-2164-10-153.
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.
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.
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.
证明基因表达微阵列结果的可重复性能力是微阵列技术在临床应用中使用的关键考量因素。虽然研究表明在给定条件下微阵列数据可以“高度可重复”，但在用于表征和表达测量性能的各种指标和术语之间几乎没有定量比较的能力。使用标准化的概念工具可以极大地促进微阵列领域的用户、开发者和监管利益相关者之间的沟通。虽然计量科学（计量学）受到复用程度较低的系统的影响，但它致力于建立一个连贯且国际认可的词汇表和定量实践，以表征测量过程。
计量学概念“准确性”的两个独立方面是“真实性”（测量值与公认参考值的接近程度）和“精密度”（测量结果彼此之间的接近程度）。一项精心设计的合作研究能够估计各种基因表达测量精密度指标：重复性、几种中间精密度类型以及可重复性。2004年的三项表达分析试点能力验证合作研究，每项研究有13至16名参与者，对两个参考RNA样本库中的每一个都进行了三次微阵列测量。通过使用并适度扩展一致认可的ISO 5725文件标准，我们评估了单个微阵列信号测量的计量学精密度品质因数，从适用于单个测量过程的计算开始，例如微阵列上单个探针的技术重复表达值，到表示给定平台中所有探针的精密度函数的估计和展示。
只需适度扩展，既定的计量框架就可以有效地用于表征微阵列和其他高度复用系统的测量性能。精密度函数展示了作为信号水平函数从对一种或多种参考物质进行适当重复测量估计出的常规精密度指标，值得进一步开发以表征测量平台、监测测量系统性能的变化以及比较不同实验室或分析人员之间的性能。
