Microarray Scanner Performance Over a Five-Week Period as Measured With Cy5 and Cy3 Serial Dilution Slides

To investigate scanner performance and guide development of an instrument qualification method, slides with replicates of successive dilutions of cyanine 5 (Cy5) and cyanine 3 (Cy3) dyes (referred to as dye slides) were scanned. The successive dilutions form a dose-response curve from which performance can be assessed. The effects of a variety of factors, including the number of scans and slide storage conditions, on scanner performance over a five-week period were investigated and tracked with time series charts of dye signal intensity, signal-to-noise (S/N), signal background, slope, and limit of detection (LOD). Scanner drift was tracked with a known stable reference material, Standard Reference Material (SRM) 2242. The greatest effect on the figures of merit was the dye, with the Cy5 dye showing signs of degradation after one week of scanning independent of all other factors while the Cy3 dye remained relatively stable. Use of the charts to track scanner performance over time holds promise for development of a method for microarray scanner performance qualification. Although not a prescription for performance qualification, this introductory study provides sufficient information regarding the use of dye slides to enable the user to institute a preliminary test method.