Assessment Of Microarray Technology Using MAQC Samples
Introduction
Recently the MicroArray Quality Control (MAQC) consortium published the most comprehensive study to date assessing the performance and cross platform comparability of microarray data (MAQC Consortium. Nat. Biotechnol. 24:1151-1161 (2006)). This study laid a foundation and framework for assessment of microarray performance, whether for proficiency testing, or for assessing changes to microarray platforms. The commercially available samples and the metrics used in the study, as well as the large reference dataset generated by the study, allow for the relatively straightforward assessment of microarray performance.
As demonstrated in the MAQC study, microarray performance is generally achieved through balancing factors such as sensitivity, accuracy and reproducibility. Platform design choices that emphasize one aspect tend to do so at the expense of the others. The Agilent Technologies (Palo Alto, CA) microarray platform seeks to achieve an appropriate balance among these attributes, with an emphasis on accuracy and sensitivity of detecting differential expression across a wide dynamic range. The results of these design choices can be seen in the data presented in the MAQC study.
Through technology enhancements that allow for 4 individual whole genome microarrays to be printed on a single glass slide, we have improved both the sensitivity and reproducibility of the platform without sacrificing the accuracy of differential expression calls. Due to the reduced surface area of the array, an increased concentration of sample can be hybridized without increasing sample input requirements. Signals that might otherwise have been lost due to scanner saturation are captured by scanning at high and low gain settings using the new eXtended Dynamic Range (XDR) feature of the Agilent microarray scanner. Combining the feature intensity data from the two different scans is accomplished automatically with Agilent Feature Extraction software (v9.1 or higher).
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