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DNA Software > Products > Visual OMP > Case Studies > Microarray Probe Analysis

Microarray Probe Analysis

Reduce False Positive and False Negatives with Powerful Cross-Hybridization Analysis

Fast and accurate detection of bacterial and viral pathogens is an absolutely critical function for a successful rapid biodefense response. While oligonucleotide microarrays hold great promise in helping to meet the need for pathogen detection and strain identification, microarrays often suffer from poor specificity and inconsistent sensitivity. False positives and negatives can be avoided by utilizing Visual OMP to increase the quality and performance of DNA probes while simultaneously avoiding cross hybridization and mishybridization.

In the published study cited here a microarray was designed to rapidly identify which strain of the Rotavirus pathogen was present in an unknown sample. Visual OMP was used to simulate microarray performance with actual probe designs and target information. A comparison of the Visual OMP results with experimental data clearly reveals how Visual OMP can reproduce the microarray’s performance detecting various rotavirus strains, enabling the ability to perform in silico optimization of the microarray design before a single laboratory experiment is started.

Visual OMP was used to simulate the results from a study by Chizhikov*. The screen shot on the left shows the cross-hybridization calculations from Visual OMP using selected probes from the experiment. On the right is the scanned image from the published microarray experiment with Visual OMP predicted values over layed.

* Chizhikov, et al.: Detection and Genotyping of Human Group A Rotaviruses by Oligonucleotide Microarray Hybridization. Journal of Clinical Microbiology, July 2002, p. 2398–2407. Vol. 40, No. 7.