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In Bid to Court Cancer Cyto Community, OGT Prepares CCMC-Designed Chip for Launch


Oxford Gene Technology said this week that it has signed an agreement with the Cancer Cytogenomics Microarray Consortium to use the organization's suggested cancer array design to develop and launch its own whole-genome, cancer-specific chip.

According to OGT, the new array will include probes for more than 500 cancer genes and 130 cancer-associated genomic regions from the CCMC's design for hematological and solid tumors. In addition, the licensing agreement gives OGT the right to promote its new product as being based on the CCMC design, making OGT one of two firms, along with Agilent Technologies, to be able to market its chips using CCMC's name.

Ruth Burton, product manager of OGT's CytoSure array menu, told BioArray News this week that the new chip should become available by the end of this year. While OGT already offers several cancer-focused arrays designed specifically for cytogenetics research laboratories, Burton said the CCMC-based array should "appeal to a broad range of researchers, particularly members of the CCMC consortium."

The CCMC consists of clinical cytogeneticists, molecular pathologists, and molecular geneticists who are interested in applying microarray technologies to cancer diagnosis and cancer research. Within a year of its founding in 2009, the organization had devised a consensus design for cancer cytogenetics research (BAN 11/30/2010).

Marilyn Li, a former president of the organization and director of the Cancer Genetics Laboratory at Baylor College of Medicine, told BioArray News this week that she believes that the CCMC design is "very good for cancer" as it "not only focuses on cancer genes but also covers the whole genome." Acknowledging a personal bias toward her organization's array design, Li said that she prefers to use the CCMC-designed array for all of her cancer patients.

Still, Li added that continuous improvement of the CCMC array is "needed and ongoing," a sentiment shared by OGT's Burton, who described the content of cancer-specific chips as "continuously evolving." But given the role that the CCMC has played in fostering the adoption of chromosomal microarrays for cancer cytogenetics, Burton said that the design is an "amalgamation of many years of research," and that it provides a "standardized design for all scientists working with cancer samples."

Other Chips

Oxford, UK-based OGT has been relatively active in developing the market for cancer cytogenetics arrays. With this market segment in mind, the firm launched two chips last year. In March, it rolled out its CytoSure Hematological Cancer+SNP array, a tool it designed to study a number of hematological malignancies, including chronic lymphocytic leukemia and multiple myeloma (BAN 3/6/2012). That chip is available in an 8x60K format, meaning that each slide contains eight distinct arrays of 60,000 markers.

And in June, it introduced another array called Cancer+SNP that contains copy number variants and SNPs covering 1,500 cancer-related genes, with enhanced coverage of 17 select genes (BAN 6/26/2012). That chip, developed with researchers at the University of Lausanne in Switzerland, is available in Agilent Technologies' 4x180K format, meaning that four 180,000-marker arrays are available on each microarray slide. Agilent manufactures OGT's arrays, and OGT is an Agilent-certified service provider.

Burton said that OGT expects demand for these other arrays to continue, despite the availability of a CCMC-based array. "While there is often consensus amongst researchers on key genomic regions to cover, individual researchers often have additional regions of interest," Burton said. Because of this, OGT will "continue to offer additional cancer-focused arrays, such as the CytoSure Haematological Cancer+SNP array, which has high-resolution coverage of a number of common hematological cancers," she added.

By taking a license to sell a CCMC-based array, the firm could gain a marketing advantage. At the same time, other vendors have expressed reservations about selling CCMC-designed arrays, arguing that their products already cover much of the same content, or even more. A representative for Cambridge, UK-based BlueGnome, now an Illumina company, told BioArray News last summer that the firm's CytoChip Cancer product includes 670 cancer genes, "many of which will be in common" with the CCMC's design.

And Richard Shippy, Affymetrix's former director of strategic product marketing for clinical applications, similarly told BioArray News last year that the company's 2.6-million-marker CytoScan HD offering "covers every gene in the genome," including the CCMC's list (BAN 8/14/2012). Shippy has since joined Illumina as director of global product marketing for clinical genomics in the diagnostics division.

While these other vendors have yet to introduce CCMC-based designs, Burton said that OGT's product would be competitive against rival offerings, including Agilent's, because of the firm's "rigorous" probe optimization procedures, in which the best performing probes from a database of more than 23 million pre-optimized probes are selected for inclusion in its products.

She also noted that OGT CGH+SNP array users can use any reference sample in their experiments, in contrast to other platforms, and said that in OGT's workflow there is "no need to digest the DNA or change the existing array comparative genomic hybridization protocol." Another attribute the firm sees as an advantage is its CytoSure Interpret software. Burton cited recent internal marketing research that showed that the firm's software is the primary reason its customers choose to use OGT arrays versus competitors'.

It is advancements in bioinformatics that OGT believes will help expand the market for cancer-specific arrays, according to Burton.

"It is not only the improvements in content that are driving the increase in demand; improvements in interpretation is also an important factor," Burton said. "More information than ever before is now available, allowing researchers to investigate the impact of different treatment regimes and associated prognosis," she said. "For these reasons, we expect the uptake of cancer arrays will be relatively rapid."