Microarray Cross-platform Study

Agilent Technologies Inc. has announced that the first objective comparison of its kind of tiling microarray array platforms using
engineered DNA targets demonstrated the high performance and cost effectiveness of Agilent microarrays.
Unlike previous evaluations, the composition of the spike-in DNA in this study was engineered to mimic chromatin immunoprecipitation (ChIP) or copy-number amplification experiments across a wide dynamic range. To ensure a fair evaluation, the composition was not disclosed to participants. This made it possible to quantitatively evaluate each platform’s sensitivity and specificity of detecting and quantifying a predefined standard without bias.
First, platforms were compared using their highest possible tiling density. In evaluating results from comparable algorithms, Agilent
consistently achieved the highest or equivalent scores, but did so with fewer probes, half as many replicates and less sample DNA than either of the other platforms.
Overall, the study found that longer oligonucleotide (60-nt) microarrays, such as Agilent’s, were more sensitive at detecting very low enrichment or copy number. Additionally, Agilent demonstrated the highest levels of sensitivity and specificity per probe, in some cases
by orders of magnitude, over a range of simulated tiling densities.