Gene-specific analysis

Gene-specific information is frequently used for interpretation of anomalies detected with aCGH and SNP arrays. Knowing particular genes covering a region of specific copy number change can be especially valuable when dealing with micro-alterations. To make this knowledge more targeted oneClickCGH and CGH Fusion provide their users with an ability to quickly short-list the genes involved in a particular copy number or LOH pattern. A list of affected genes can be obtained for a single sample as well as for an aberration frequency profile across multiple samples.

Simple short-listing of affected genes though may lead to a fairly large set of information, which sometimes becomes useless, especially if large anomalies are present. That is why infoQuant has developed a unique statistical method of computing gene significance that puts genes affected by observed anomalies the most at the top of the list. Power of this method comes from its use of CNV frequency data pre-computed based on HapMap samples. This technique makes sure that the genes least likely to be a part of a CNV in a normal sample will attract user’s attention first and the interpretation process will take the least amount of time possible.

Our significance table also provides information about significantly affected disorder categories and Gene Ontology terms making sure that no important biological information is missed when analyzing a copy number or LOH pattern.

This tool built right into infoQuant software is capable of bringing aCGH Copy Number reporting procedure of a Cytogenetic laboratory to the next level of efficiency.