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OGT Calls WTCCC Copy Number Variation Study a 'Step Change' for Its Services Business


After years of performing lower-throughput array studies for customers through its services business, Oxford Gene Technology is now preparing to take on higher-throughput efforts to make use of its newly established automated array-processing infrastructure, according to a company official.

John Anson, director of R&D at the UK firm, told BioArray News this week that the lab automation and protocols that the firm put in place to process samples for a copy-number variation study undertaken by the Wellcome Trust Case Control Consortium have changed OGT's business, leading it to solicit more large-scale projects.

OGT recently completed in 20 weeks the processing for more than 20,000 WTCCC samples using whole-genome human CNV-focused arrays manufactured by Agilent Technologies as part of an effort to identify genetic variants involved in such conditions as bipolar disorder, Crohn's disease, coronary artery disease, type 1 and 2 diabetes, rheumatoid arthritis, breast cancer, and hypertension.

OGT processed the samples as an Agilent certified service provider (see BAN 8/5/2008).

To handle the study, OGT used Agilent’s hybridization oven, scanner, and slide carousel, together with SciGene’s Little Dipper processor, and the Velocity 11 Bravo, a robotics platform acquired by Agilent in 2007 that automates most of the steps in the labeling process from dispensing the DNA from its original plate into new plates through labeling. Additionally, OGT developed a custom laboratory information management system. OGT said it performed and recorded 40 quality-control checks for each sample during the project.

"Services have always been an important part of OGT's offering because they are a source of revenue but also because it provides the company with access to high-quality research projects with academic researchers and enables us to open up new windows for the application of microarrays," said Anson.

To date, most of the projects handled by OGT's service unit were "relatively low throughput" and were processed in a "very manual way," he said. The WTCCC project gave OGT the ability to "look at step change in services offering, going from manual to an automated, high-throughput approach," he said. "We had to adapt our processes and the way people in OGT services operate to provide huge amounts of high-quality data in a short period of time."

Part of that expansion was new hires. Anson said that OGT hired seven new personnel to run the WTCCC project. The company has retained most of those and the others are available to supplement OGT's workforce on a temporary basis as large projects come along.

"We had to recruit additional staff that were appropriately trained and were competent," Anson said. "We are also now able to go out and tap into [the] temporary workforce. There is a lot of skill available in the biotechnology space in Oxford, so if we need to add people in a short time, we are very confident that we are able to go do that."

The most important change for OGT, though, was that it acquired the skills to attract projects of a similar size — and not only in surveying CNVs, Anson said. "Now that we know we can run samples in a high-throughput manner, the ability to transfer that knowledge to other applications is also there. We can expand our expertise to gene expression, methylation profiling, and microRNA studies as well. "There is a lot we have done in the CNV area that can translate to other areas," Anson added.

One possible tie-in for the firm's new high-throughput infrastructure is Sense Proteomic, a protein array company that OGT acquired earlier this year with the plan of using Sense's technology in biomarker discovery programs (see BAN 3/17/2009).

"The high-throughput array facility allows us to run projects with clinical collaborators to take those samples and run them to produce data in relation to our own in-house discovery programs," said Anson. "Since Sense is moving into biomarker discovery, we can use our facilities to run both our services business and microarrays to establish DNA content for Sense.

"We are in discussion with a number of potential collaborators with access to numerous disease cohorts, so this is a very interesting area for us," he added, without elaborating.

According to Anson, OGT has also examined the idea of exporting its high-throughput setup to another location. Hypothetically, he said, the firm could replicate its lab in, say, the US or Japan to handle a large project as it comes along.

"Basically, we have designed a package that we can take to other parts of the UK and around the world and utilize it in that other location," he said. Anson said that OGT currently has no plans to set up shop at another location, however.

While Anson stressed that OGT sees such large-scale projects as vehicles to product development, he maintained that OGT has no plans to move into the CNV array market. Agilent this year has launched two CNV-focused arrays for association studies, one of them based on the WTCCC's design. A third array is planned to launch this summer (see BAN 4/7/2009).

OGT currently offers arrays for such applications as comparative genomic hybridization and chromatin immunoprecipitation (ChIP)-on-chip. The firm has launched several arrays for the detection of chromosomal abnormalities via its CytoSure family of chips. These areas will remain the focus for OGT, Anson said. At the same time, he noted, the firm could host other CNV association studies.

"We are not focused on developing a research use CNV array," Anson said. "We do have a strong relationship with Agilent and this project was with Agilent as we are a certified service provider. We are certainly talking with them about other opportunities in this space."