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OGT to Upgrade Chromosomal Microarray Analysis Software


By Justin Petrone

Oxford Gene Technology will later this month release an upgraded version of its CytoSure Interpret software for array comparative genomic hybridization analysis.

Ruth Burton, OGT's product manager for clinical solutions, discussed the new software at the American College of Medical Genetics' annual meeting, held last month in Charlotte, NC. An OGT executive this week discussed the pending software launch with BioArray News.

James Clough, vice president of clinical and genomic solutions at OGT, said that the UK-based firm considers its software offering to be a "key differentiator" in the market for chromosomal microarrays, and that its customers have told it that software is a "critical factor" when deciding on an array platform.

Other companies in the space also see software as an avenue to reaching customers. Cambridge, UK-based BlueGnome, for instance, which sells a menu of arrays for cytogenetic research, originally started out as a software firm, and offers an array analysis tool called BlueFuse Multi (BAN 3/17/2009).

OGT entered the cytogenetics market with the release of its first CytoSure arrays in 2007. The firm launched its CytoSure Interpret software two years later (BAN 12/15/2009).

According to Clough, the fourth version of CytoSure Interpret is provided free of charge to the firm's array customers and existing users can contact the firm to upgrade to the new software.

Clough called the new version a "significant change" compared with previous versions, and noted that it features an SQL relational database, whereas the previous version had an XML-based database. This means that sample data can be stored and analyzed based on its relationship with other data. Samples can be segregated into different projects by sample type or by user, "simplifying" the analysis, Clough said.

The software is preloaded with all of OGT's catalog array design files, he said. Sample annotation is user-definable and custom annotation combined with new advanced search and filtering tools support data retrieval. Studying inheritance patterns has also been "simplified" as samples can be linked using the software's new Family Tree viewer.

CytoSure Interpret also includes annotation tracks covering syndromes, genes, exons, copy number variation, and segmental duplication that link to publically available databases such as ISCA and Decipher. Data can be exported in a variety of formats allowing it to be uploaded into external databases, Clough said.

Additionally, the new software takes into account two of OGT's most recently introduced arrays, its CytoSure ISCA+SNP array for constitutional cytogenetics and its CytoSure Haematological Cancer +SNP array.

Since adding SNP content to its arrays, OGT has improved the algorithm that identifies regions of loss of heterozygosity, Clough said. Continuous regions of homozygous probes are given a score that can be used to identify significant regions. "We have also improved the ability of the software to discriminate between the two SNP alleles, reducing the number of false calls," he said.

The software also includes cancer annotation tracks that can be selected during installation to provide direct links to chronic lymphocytic leukemia regions from the National Institutes of Health's Mitelman database, the Cancer Gene Census, and the hematology regions from the Atlas of Genetics and Cytogenetics in Oncology and Haematology.

"When analyzing cancer samples it is important to assess the biological significance of any aberrations present," said Clough. "These [annotation] tracks aid in the analysis of by highlighting important regions, and, in the case of the Mitelman database, relate chromosomal aberrations to specific tumor characteristics."

The cancer annotation tracks will also support the analysis of forthcoming OGT arrays. Clough said last month that the firm will launch a number of oncology-focused arrays during the year (BAN 3/6/2012).

Have topics you'd like to see covered in BioArray News? Contact the editor at jpetrone [at] genomeweb [.]com

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