Dated: 5/17/2007
By Stephanie Fulmer-Smentek, Anne Bergstrom Lucas, Petula D’Andrade, Athene Chan, Alex Wong, Xiangyang Zhou and John Corson. Agilent Technologies.
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, and 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 a balance among sensitivity, accuracy and reproducibility. Platform design choices that emphasize one aspect tend to do so at the expense of the others.
We have designed our microarray platform to achieve an appropriate balance among these different performance attributes with a strong 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 four 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 the latest version of the Agilent Feature Extraction software (v9.1).
We have used the commercially available MAQC samples to evaluate the performance of Agilent’s new high density multi-pack whole human genome arrays (4-Pack). Using some of the analysis methods and metrics put forth in that study, we compare the performance of the new generation microarrays to the “legacy” whole genome products (44K).
While our previous generation microarrays demonstrated outstanding sensitivity in the MAQC study, the new 4-Pack microarray extends in sensitivity and dynamic range of differential expression detection.
Accuracy is further improved in the new 4-Pack format and reproducibility of signal shows significant improvement, with median interarray CVs less than 5%.
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