Medium-resolution arrays

Many specialists may think that medium-resolution array CGH datasets (1,000-20,000 probes or clones per array) are much easier to analyze than high density data. This may be true in some aspects of computational efficiency and resource management, however, we at infoQuant realize that there are very important specifics of BAC data processing, which should be addressed. Especially, if BAC arrays are intended for use in clinical Cytogenetics. Targeted BAC arrays are irreplaceable in diagnosis of many critical disorders, as  measurements extracted from them are usually relatively straight-forward to interpret. But they also require a very special data analysis workflow in order to produce high-quality data. infoQuant has been working with many Cytogenetics laboratories for several years in order to refine that workflow.

Utilization of on-slide replicates and dye-swap technique are frequently employed in BAC experiments to increase Signal-to-Noise ratio. infoQuant software is capable of utilizing such data and extracting clone-wise log-ratio measurements in a way most beneficial for Copy Number detection and reporting.

Appropriate data QC and image analysis may greatly increase reliability of BAC data in clinical tests. oneClickCGH provides its users with both capabilities.

In a medium-resolution experiment it is very important to be able to visualize data from every single clone in a simple, but interactive manner. Users of oneClickCGH can access many categories of measurement and annotation data for all clones through our intelligently built ratio plot. They can even manually omit or include any selected clone during the analysis.

Finally, the versatility of reporting features plays a very important role in BAC tests. We invested a significant amount of time making sure that our various report formats (Word, PDF, Excel) include all information a cytogeneticist might need, includng genes, CNVs and related syndromes, and at the same time are straight to the point. The automated, yet fully interactive way of building a cytogenetic report guarantees that only relevant copy number changes get reported.