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Targeting Custom Market, OGT Offers Probe Design Database for CGH, ChIP, Methylation

Oxford Gene Technology upgraded its service offering last week by releasing a database of more than 10 million oligonucleotide probes for use in custom array comparative genomic hybridization projects.
OGT said its customers can request arrays by region of interest or a list of genes, which the company will design using its Oligome database. There will be no additional fee for array CGH, OGT said. The 60-mer oligo arrays will be manufactured by Agilent Technologies and returned to OGT’s headquarters in Oxford, UK, where the firm will either run the arrays itself or distribute them to its customers.
While OGT is initially targeting the Oligome database to array-CGH users, the company also offers ready-made probes for other application areas where it has expertise, such as chromatin immunoprecipitation-on-chip and methylation profiling, a company official said.
James Clough, the firm’s commercial director, told BioArray News last week that in addition to CGH, the company will use Oligome to design arrays for customers involved in ChIP or methylation-based studies, though he noted that OGT still needs to design extra probes for these applications.
Oligome currently does not support the design of expression or miRNA arrays, but Clough said the company plans to enable those applications in the database
Clough said that Oligome grew out of an increasing need to quickly turn arrays over to researchers and to OGT’s longstanding relationships with its customer base. For example, OGT has provided custom CGH arrays to Oxford Genetic Knowledge Park, a state-funded research organization dedicated to developing new tools for cytogenetic use (see BAN 2/14/2006).


OGT said it is using Oligome as the foundation for its free probe-design service, which it believes will save customers time and the need to consult with internal bioinformaticists.
“We’ve got a massive amount of probe-design expertise at OGT and so we’ve used our knowledge to build this database,” Clough said. “What we’ve realized through interaction with customers is that they are not all bioinformaticians. They want an array designed to meet their requirements but not to get too involved on the design side.”
Clough said that the opportunity to leave the probe design to OGT will give the company an advantage in the custom array market because other companies, like Agilent Technologies, offer custom-design capabilities that require a higher level of bioinformatics knowledge. While other services count on the researcher to upload or design probes for their arrays, OGT’s service saves users that step should they wish to skip it.
By cutting out the barriers to designing chips, OGT believes it has the opportunity to reach more customers who may have found the process of array design to be too time and resource-consuming.
“The challenges of scientists being able to keep up with all the movement in array design and applications are big,” said Clough. “It is difficult to generalize about life science customers, but the vast majority of customers are looking to use array CGH as a tool in their research but lack the bioinformatics expertise to do the design portion,” he said. Clough claimed that OGT can design arrays “in minutes” using the Oligome database.
Agilent and NimbleGen
OGT signed an OEM and service provider partnership agreement with Agilent earlier this year and is touting the firm’s multiplex array formats and printing technology as part of the new offering. Agilent currently offers arrays with densities up to 244,000 features per chip, and offers formats of two, four, or eight arrays per printed slide (see BAN 1/16/2007).
At the same time, by targeting methylation, array CGH, and ChIP customers with a new design tool, OGT is competing in the same space served by Agilent’s online eArray chip-design tool, which allows customers to design arrays that can be manufactured by Agilent.

“The challenges of scientists being able to keep up with all the movement in array design and applications are big.”

Clough said that OGT’s customers might find Oligome more efficient than eArray because eArray requires users to select probes from a database or upload their own probes, whereas OGT can generate chips automatically based on regions of interest.
“We are saying that if you give us the regions of interest, we will use the Oligome database to design an array for you,” Clough said. “We can send the design back with our visualization software and then the customer looks at what the coverage is and they don’t have to worry about how we got to the probes.”
Jay Kaufman, senior director of genomics marketing at Agilent Technologies, told BioArray News in an e-mail this week that while it could be perceived that OGT’s Oligome database competes with eArray, “eArray will appeal to a broader segment of the market” by offering capabilities for designing copy number variation arrays.
“In the area of aCGH, these two tools do seem to offer the customer similar capabilities. However, as we continue to expand on our portfolio for studying copy number variation, we will also expand our current database of probes in eArray,” he wrote.
Kaufman also said that the Oligome database launch actually benefits Agilent’s effort to “expand our market penetration through a variety of partnerships and channel options.” He said that the partnership with OGT is “very synergistic” and that there are other business areas where the two companies are cooperating.  From Agilent’s perspective the supply of arrays to OGT is therefore one aspect of a broader relationship.
Oligome will also compete with design capabilities offered by Roche NimbleGen, which has built part of its business on custom array projects such as array CGH, methylation profiling, and ChIP-on-chip.
NimbleGen spokesperson Joleen Rau told BioArray News this week in an e-mail that for human CGH projects, the firm can select from a set of 420 million probes, 22 million of which have been “empirically tested to cover any targeted region with any density required.” 
She added that the “flexibility and high information content provided by Roche NimbleGen’s microarray technology enables genome-wide and targeted detection of copy number variation at the highest resolution current available.”

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