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BlueGnome, Expanding Cyto Menu, Debuts High-Resolution, 850K SNP Chip on Illumina Platform

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This story was originally posted on June 14.

Laboratories that would like to use a high-resolution SNP microarray for constitutional and cancer cytogenetics now have more choices.

BlueGnome, the Cambridge, UK-based biotech that Illumina acquired last year, recently added a high-density, Illumina-manufactured SNP chip to its menu of cyto arrays, according to Greg Heath, senior vice president and general manager of Illumina's Diagnostics business.

Heath told BioArray News last week that the chip, which BlueGnome launched earlier this year, contains copy number content selected from International Collaboration for Clinical Genetics, the Cancer Cytogenomics Microarray Consortium, and other sources, in addition to SNP content. Each chip hosts eight separate arrays of 850,000-markers. He declined to discuss pricing.

"We tried to include content from two areas, the ICCG and the CCMC," Heath said. "This is a research product, and we see people doing cytogenetic research in both developmental delay and cancer," he said. "We wanted to give them the opportunity to do both on the same array."

Constitutional and cancer cytogeneticists currently have a number of arrays to choose from. Some opt to use lower-density, Agilent Technologies-manufactured comparative genomic hybridization arrays, some of which also include SNP content, including those designed and sold by BlueGnome. Others have decided to use higher-resolution SNP arrays, such as Affymetrix's 2.7-million-marker CytoScan product.

The availability of another high-resolution SNP array should give customers who might prefer an array like CytoScan another option.

BlueGnome also now sells Illumina's InfiniumDx CytoSNP-12 platform for constitutional cytogenetics. The company earlier this year filed the 300,000-marker microarray with the US Food and Drug Administration to be cleared for clinical use (BAN 4/23/2013). Heath described discussions with the FDA as "ongoing," and said the company continues to work with the agency on the filing, but did not elaborate.

Heath described the content on the CytoSNP-12, which is focused specifically on constitutional testing, as "more conservative" than the 850K, given that the markers on an array that goes through clinical trials must be "more robust." The 850K meantime is targeted to researchers who want "current, state of the art content." And, according to Heath, customer response to the array so far has been "positive."

"There is always a need in the market for a cutting edge array that casts a wider net," said Heath.

Another reason customers may be warming to the 850K is that cytogeneticists who use arrays for detecting constitutional aberrations are eager to adopt array technology for cancer, but have been hesitant to validate it on a separate chip, Heath said.

He noted that with a dual-use array, such as the CytoSNP-850K, a user could run seven constitutional and one cancer in the same assay, rather than running two separate arrays, one specifically for constitutional research and the other focused on oncology.

"It allows for diversity," said Heath. "Cyto labs might want to run multiple research projects at the same time."

He noted that the company will continue to sell Agilent Technologies-manufactured arrays to its customer base. Prior to the Illumina acquisition, Agilent had manufactured menu of BlueGnome's CytoChips, such as its CytoChip ISCA and CytoChip Focus arrays. BlueGnome internally manufactures the bacterial artificial chromosome arrays sold in its 24sure kits for pre-implantation genetic screening.

BlueGnome customers who use its 24sure BAC arrays as part of in vitro fertilization processes will also soon have the ability to adopt Illumina SNP arrays as well. Heath said that the company is developing a new array-based offering called Karyomapping that will allow single-gene preimplantation genetic diagnosis and screening.

He declined to provide a launch date for Karyomapping.

'Along the Continuum'

Illumina paid $88 million to acquire BlueGnome last year (BAN 9/25/2012). At the time of the deal, company executives said that Illumina was enticed to buy BlueGnome because of its BlueFuse software, which provides reporting capabilities, access to external annotation sources, and the option to visualize data in the context of previously processed samples.

"One of the reasons we acquired BlueGnome is because of its software expertise," Heath said. He said that the company believes that customers who are familiar with the features and functionality of the software should be able to use it as much as possible.

BlueGnome currently markets all of its arrays, in addition to its BlueFISH fluorescence in situ hybridization probes, as part of one offering for cytogenetics that is supported by its BlueFuse software.

Depending on a customer's interest, he or she can use 24sure, CytoChip Focus and ISCA, as well as Illumina's existing CytoSNP-12 and the new CytoSNP-850K to conduct experiments, while continuing to use BlueFuse, according to the firm's marketing materials.

And, according to Heath, the firm is interested in enabling its customers to move to next-generation sequencing, should they desire to, while continuing to use the same BlueFuse software.

"There's a lot of research that is shifting to sequencing," said Heath. "We try to stay abreast of where the market is going, rather than trying to push a particular technology."

The company is positioning both its array and sequencing platforms for use in the reproductive health market. Earlier this year, it acquired Verinata Health, a provider of sequencing-based, non-invasive prenatal testing. Company executives have since mentioned that the capabilities of BlueGnome and Verinata could complement each other.

"We think about it along the continuum of reproductive health," said Heath of the firm's recent acquisitions. He described a scenario where women could use the company's cystic fibrosis carrier screening assay prior to conception, and then, should they experience trouble becoming pregnant, could opt for 24sure as part of an IVF cycle. Expectant mothers concerned about the health of their unborn child could then request testing through Verinata. And children suspected of having developmental delay or other genetic abnormalities could later be tested using BlueGnome's menu of cyto arrays.

Looking ahead, he said that it is possible that BlueGnome's ability to screen single cells, which currently employed in its 24sure offering, and Verinata's ability to test cell-free DNA could also be applied in cancer research.

"We now have technical knowhow we can apply in that space as well," he said.

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