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OGT Debuts Cyto CGH and SNP Array for Hematological Cancers; Plans More Oncology Chips


By Justin Petrone

Oxford Gene Technology will later this month introduce an array with copy number variant and SNP content that it claims can be used to study a number of hematological malignancies, including chronic lymphocytic leukemia and multiple myeloma.

Additionally, the new array includes content that can be used to investigate myeloproliferative neoplasms and myelodysplatic syndromes.

James Clough, OGT's vice president of clinical and genomic solutions, said that the new array is targeted to cytogeneticists that are using older technologies, such as fluorescence in situ hybridization or microscope-based molecular karyotyping. He said that this previous work informed the design of the array.

"Cytogeneticists have been analyzing hematological cancers using standard cytogenetic techniques for many years and, as such, they are particularly well characterized with well-defined chromosomal gains and losses," Clough told BioArray News.

He said that the chip, called the CytoSure Haematological Cancer +SNP array, targets genomic regions "known to be important predictors of disease progression and patient prognosis," while providing "good backbone coverage" of the genome. OGT worked with several collaborators on the design of the array, but Clough declined to name them.

It is one of a number of cancer-focused arrays that OGT plans to launch in coming months for the "genetic analysis of cancerous lesions." Clough said that these new arrays will cover a "broader range" of cancer types, but did not elaborate.

By launching the array, OGT will be expanding its CytoSure menu to include tools for cancer cytogenetics research. The Oxford, UK-based company offers a number of focused arrays for cytogenetics and molecular genetics research.

There is no dearth of cancer-focused arrays targeted to the cytogenetics research community. Ambry Genetics rolled out its CancerArray service last September, offering a 180,000-probe array with coverage across the genome (BAN 9/13/2011). Others marketing cancer-focused offerings either as kits or services include BlueGnome, PerkinElmer, and CombiMatrix. And Affymetrix has said that its CytoScan HD array could be used in cancer cytogenetics research (BAN 1/17/2012).

One offering that is more directly competitive is CombiMatrix's Heme Profile, which is intended for studying CLL and other hematologic malignancies, according to the Irvine, Calif.-based company's website.

Agilent Technologies manufactures CombiMatrix's chip on a 180,000-marker CGH platform. Agilent also manufactures OGT's array, but OGT's array also includes SNPs that allow it to pick up loss of heterozygosity, a common occurrence in cancer that indicates the absence of a functional tumor suppressor gene in the lost region.

Agilent began offering its new CGH+SNP array format last year (BAN 10/11/2011). In its most recent earnings call, CombiMatrix CEO Judd Jessup said that the company plans to include SNP content in its array services in the coming months (see related story, this issue).

BlueGnome last year introduced its CytoChip Cancer array on Agilent's CGH+SNP platform, but the array, which is based on a consensus design set by the Cancer Cytogenomic Microarray Consortium and covers 670 cancer-related genes, is not specifically designed to use in investigating hematological malignancies.

According to Clough, CGH has to date been the favored technique for array-based CNV detection. Customers who wanted to detect LOH regions opted to use SNP arrays, like Affy's SNP 6.0 Array, as a complementary platform.

"Until recently it was not possible to combine this technique with SNP analysis and LOH detection, meaning either two separate arrays were needed or inferior SNP-based CNV detection platforms were used," said Clough. He noted that the inclusion of SNP probes on the array does not affect the performance of the assay or require other protocols.

"Due to the unique design of the SNP probes, where an intensity-based comparison is made between the two SNP probes, there are no changes to the standard CGH protocol, no restriction digest is required, and any reference sample can be used," said Clough.

He said the availability of CGH and SNP probes on one array would be "cost effective" for users, although he declined to answer a question about array pricing.

Regarding the competition, Clough also said that OGT's CytoSure Interpret software could distinguish the firm from rivals. He noted that recent enhancements to the software include the addition of extensive cancer-specific annotation tracks providing results in context.

To promote the new chip, OGT plans to hit the road. Clough said the firm will be discussing its new offering at several meetings. The firm said it will attend the International Society of Cellular Oncology Congress in Mallorca, Spain; the UK Cancer Cytogenetics Group Meeting in Birmingham; and the Australian Society of Cytogenetics Meeting in Port Stephens, Australia, all of which are scheduled to take place in the next few weeks.

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