LOH detection for SNP arrays
LOH detection is a very important aspect of array-based cancer research and diagnostics. infoQuant has utilized its expertise in robust non-parametric statistics in order to build a reliable yet simple approach to LOH detection. Our software packages oneClickCGH and CGH Fusion allow users of Affymetrix and Illumina SNP arrays to highlight suspected LOH regions in a matter of seconds. This approach is based on a bootstrap procedure that attempts to estimate distribution of allele-specific measurements in “normal” regions and uses that estimate to detect Loss of Heterozygosity along genome. Several iterations of bootstrapping in combination with the results of copy number change detection ensure reliability of LOH calls.
To accommodate needs of different types of users, we also provide a set of controls that facilitates filtering of detected anomalies by their size.
oneClickCGH and CGH Fusion also provide capability to filter out LOH regions frequently observed in HapMap samples to ensure that only relevant regions get detected and reported and the user does not have to deal with an overwhelming number of anomalies.