Development of OGT’s CytoSure™ analysis software for aCGH is continuing apace, with rapid implementation of customer requests a primary goal. John Shovelton, a computational biologist at OGT, explained: “We have regular contact with our customers. They can come to us and request a specific function that would be beneficial to them and, if possible, we will try to implement it and send it out with the next release.”

“Probably the most significant recent addition has been the incorporation of automatic aberration calling, which is a very attractive feature for customers. Using a circular binary segmentation (CBS) algorithm, the software can automatically identify regions which appear aberrant by looking for changes in copy number. The algorithm obviously does not tell the user which segments are relevant to them, so there are options in the software for the user to add parameters which will determine the aberrant regions. Other CGH software offering similar aberration identification takes a long time to run – over two

hours in some cases – but our CBS algorithm takes an average of just seven minutes for a 105,000 probe data set. Despite this rapid aberration identification, individually processing a large number of data sets is labour intensive, so our software allows batch processing of an unlimited number of data sets.”

John continued: “Once we had introduced automatic aberration calling, it was logical to create a database to allow customers to store the results from their analyses for comparison. The stored aberrations can be viewed as a separate annotation track, and can be edited as necessary based on subsequent findings. To make data management even more flexible, we have now introduced the ability to export data in a format compatible with the DECIPHER database. This allows data to be uploaded for easy access and sharing of data via the internet, and was something users had requested.

“We are also keen to update the software to reflect research advances, and some of our customers now use a ‘loop’ technique as an alternative to dye swap experiments, as this requires less material per sample. This technique compares the data sets of samples of three patients with different phenotypes, matching up reciprocal aberrations to identify true copy number variations, and we have developed an automated tool to accelerate the analysis.” John concluded: “This rapid response to customer needs is our main objective when updating the software. Although some of these additions might seem cosmetic, they make a big difference to the customer.”