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Following Industry Trend, BlueGnome Adds Agilent-Made Oligo Arrays to Cyto Offering

BlueGnome, a Cambridge, UK-based provider of cytogenetics research tools, this week announced that it will now offer an oligonucleotide-based array that can enable researchers to take a higher-resolution look at genomic regions associated with constitutional genetic disorders.
BlueGnome’s new product, called CytoChip Oligo, is manufactured by Agilent Technologies and intended to complement its existing bacterial artificial chromosome-based CytoChip Focus arrays for hematological and constitutional research.
For BlueGnome, the new offering, which is for research use only, is in line with two new trends in the cytogenetics community: making oligo-based arrays available to cytogenetics researchers, and hiring Agilent Technologies to produce the chips.
Over the past two years, Agilent has signed similar original equipment manufacturing deals with Spokane, Wash.-based Signature Genomic Laboratories; Houston, Tex.-based Baylor College of Medicine; and Oxford Gene Technology in the UK.
While rival array vendors like Affymetrix and Illumina each launched internally developed products for the cytogenetics research market, Agilent has preferred to remain as an OEM “foundry” for its partners’ chip designs.
Graham Snudden, vice president of engineering at BlueGnome, told BioArray News this week that the firm decided to add an Agilent-made oligo array to its menu in order to cast a wider net in the cyto-research market.
“We are committed to offering a range of products that enable copy-number imbalance to be investigated across the widest range of sample types and disease areas,” Snudden said. “For this reason it is important to have access to a complete range of array technologies in order to deliver the best performing assay for current and future applications.”
BlueGnome is currently selling the third version of its BAC v. 3.0 CytoChips, which are designed to investigate constitutional abnormalities and include 5,500 BAC clones. By comparison, the new 105,000-probe CytoChip Oligo provides up to 35-kilobase resolution.
Snudden said the two platforms work with the firm’s BlueFuse Multi software and results database. He said that both platforms deliver comparable results, and that researchers are likely to choose one over the other based on their preference for BAC-based or oligo-based arrays.
“They would be expected to give very similar results on equivalent samples,” Snudden said. For instance, “at present … there is little to choose between BAC versus oligo for post-natal constitutional samples,” he said. “Any choice is largely down to what labs have used historically and where they think they might be in future.”
Over the past few years, companies that sell arrays to the cytogenetics market have sought to highlight their platforms’ superiority over those made by rivals based on whether the chips used BAC or oligo probes.
Some shops place a premium on density and security. For instance, Oxford Gene Technology’s R&D Director John Anson told BioArray News in June 2007 that “oligos offer greater probe density and greater security and confidence in the data,” and are more amenable to the large-scale manufacturing necessary for routine diagnostic use (see BAN 6/26/2007).
Other shops are responding to growing demand for oligo-based platforms, which ultimately encouraged Signature Genomic Labs and Baylor to offer Agilent-manufactured oligo arrays, in addition to internally developed BAC platforms, in April and October 2007, respectively (see BAN 4/3/2007, BAN 10/23/2007).

“There are two major challenges associated with the routine use of oligo arrays: data analysis and management; and confirmation of results.”

“Our clients want higher resolution. They have been hearing about oligo chips from competitors and they think they are better, and in some cases they are better, depending what they are looking for,” Signature CEO Lisa Shaffer told BioArray News at the time.
The debate over Signature and Baylor’s adoption of oligo-based platforms centered on whether oligo arrays produced too much aberrant data and relied too much on crude data-analysis tools to make an accurate diagnosis. While BlueGnome’s chips are for research use only, Snudden said that CytoChip Oligo had been designed to combat similar obstacles.
“There are two major challenges associated with the routine use of oligo arrays: data analysis and management; and confirmation of results,” said Snudden. “The CytoChip Oligo platform addresses these head-on by providing a comprehensive laboratory database for samples and results, and we also offer a full tiling path library of 26,000 [fluorescent in situ hybridization] probes for follow-up purposes.”
Though BlueGnome’s new CytoChip will detect constitutional genetic disorders, the company does not at the moment intend to create oligo-based versions of its CytoChip Focus line of arrays.
In September, BlueGnome debuted BlueGnome Focus hematology array version 1.0, which is designed to investigate copy-number imbalance in 50 regions of known clinical significance and larger scale alterations in the spine. The company at the time said it expects to launch a second version of the product sometime next year with additional coverage (see BAN 9/2/2008).
“Investigation of hematology samples does not currently require a high-resolution platform; indeed it could be argued that high resolution actually complicates the process,” Snudden said this week.
One major challenge for users of the hematology chip is mosaicism associated with multiple cell populations, he said. “These requirements are currently best satisfied by BAC technology, [but] it’s important to keep all options open given the pace of change in the field,” he added
‘Supplier of Choice’
BlueGnome’s announcement this week represents the latest in a string of OEM deals Agilent has signed this year. Last month, for instance, Oxford Gene Technology launched two new chips for use in cytogenetics research, both manufactured on the Agilent platform (see BAN 11/18/2008).
And Agilent is currently manufacturing Invitrogen’s new human and mouse non-coding RNA arrays (see BAN 11/11/2008).
Chris Grimley, Agilent’s senior marketing director for genomics, told BioArray News last month that the firm’s OEM business is part of a strategy to “drive microarray volume.”
Other vendors, like Affy and Illumina, are looking towards direct sales of their cytogenetics products to drive growth.
Illumina, for example, last month launched its Infinium High-Density HumanCytoSNP-12 DNA Analysis BeadChip, a 12-sample array containing nearly 300,000 genetic markers per sample that targets cytogenetic abnormalities found in genes and disease pathways linked to mental retardation, autism, and other common chromosomal anomalies (see BAN 11/18/2008).
Illumina CEO Jay Flatley said at the time that the market for cytogenetics is “huge,” valued at about $2 billion, with array-based cytogenetic tests making up $200 million of the overall cyto-testing market and growing 20 percent per year.
Jay Kaufman, vice president of product marketing at Affymetrix, provided similar estimates of market size in a recent e-mail to BioArray News. “The microarray-specific market size is growing exponentially,” he said. “For 2009, the numbers we are considering are between $175 million and $200 million.”  
But while Illumina and Affy will duke it out with BlueGnome and others in that market, Agilent prefers to work behind the scenes, Grimley told BioArray News this week.
“We feel that we offer oligo microarray products engineered to the highest standards, which enable highly robust and reproducible results,” Grimley said. “Our strategy is to capitalize on these benefits by selling both directly to end users and by selling arrays to third parties in instances where such agreements can broaden the reach of our arrays.
“At the present time the cytogentics community has not decided on a single array design, therefore Agilent’s ability to supply high-performance custom arrays has enabled us to be the supplier of choice for many institutions, both commercial and academic,” Grimley added.
According to Grimley, the company has decided to pursue an “Agilent Inside” marketing model similar to the one pioneered by computer chip giant Intel. He said this strategy gives the firm a “broader reach into the market working with the experts in a specific niche.”
Grimley also noted that Agilent has “many products that are used by the cytogentics community, including reagents and consumables used in the processing of microarrays.” He added that cytogenetics researchers are using the company’s eArray online array-design software to create their own custom microarray designs.

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