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OGT Certified to Offer High-Throughput Agilent Array Services, Embarks on 10K Sample CNV Study

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By Justin Petrone

Hungry for high-volume service deals, Oxford Gene Technology has recently made "major" investments in automation, quality control, and personnel in order to offer high-throughput services to its customers.

These investments culminated when the UK firm was certified by Agilent last week as its first high-throughput microarray service provider.

To become qualified as a high-throughput service provider, OGT had to submit data to Agilent demonstrating the company was able to run a range of samples using an automated workflow and meet "stringent" QC metrics, according to the firm.

OGT has been an Agilent certified service provider for nearly two years, but this new designation means that it meets Agilent's standards for servicing large projects. The firm's services business received a boost last year when it generated array comparative genomic hybridization copy-number data on some 22,000 samples for the Wellcome Trust Case Control Consortium in 20 weeks (see BAN 6/2/2009).

OGT said that it has recently been awarded another high-throughput screening project involving 10,000 samples on an eight-array-by-60,000-probe chip format that it aims to process within a "couple of months." Both projects were designed to use Agilent CGH/CNV arrays to conduct so-called copy number association studies across large sample populations, and OGT has said it expects similar services deals to follow.

"CNVs have been implicated in the pathogenesis of a growing number of complex diseases, including autoimmune disease, asthma, and schizophrenia," James Clough, OGT's vice president of clinical and genomic solutions, told BioArray News this week. "There is much more work to be done to enable the transition of CNV studies to routine clinical testing and large sample number cohort studies are vital to ultimately achieve patient benefits."

Such large projects are driven by the availability of Agilent's relatively new SurePrint G3 arrays for CGH and CNV studies. During the course of 2009, the Santa Clara company debuted three catalog arrays for researchers investigating the role of CNVs in human disease. Specifically, Agilent now offers a WTCCC-designed Human CNV Association 2x105K microarray for studying associations between genomic CNVs and disease; 2x400K CNV array, which was designed to cover known CNV regions from the Database of Genomic Variants; and a million-probe CNV chip suited for discovery (see BAN 4/7/2009).

Agilent has plans to create more CNV arrays going forward (see BAN 9/22/2009).

Other firms are equally keen to cash in on demand to look at CNVs across populations. Roche NimbleGen, for instance, sells a 2.1-million feature array and a chip with three 720,000-feature arrays containing CNVs that could be implicated in diseases such as autism, schizophrenia, autoimmune diseases, and HIV susceptibility. Roche partnered last year with Seoul-based services provider Macrogen to support a CNV association study led by the Korean Centers for Disease Control and Prevention (see BAN 7/7/2009).

Indeed, it helps vendors to have the capabilities in place to handle large CNV studies in order to win deals. Chris Grimley, senior marketing director for Agilent's genomics business, said in a statement that "OGT has been very successful integrating Agilent Automation Solution instrumentation and Agilent microarrays for an efficient laboratory workflow." Grimley said the company is "confident that customers will benefit from the combination of Agilent products and OGT high-throughput service."

According to Clough, OGT had to scale up its services offering, which it branded Genefficiency in October 2009, to process the 22,000 samples in the WTCCC project. Clough said that OGT made a "major investment in facilities in order to standardize and monitor the aCGH protocol and resulting data quality" from the WTCCC study. OGT's setup includes 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.

Genefficiency customers have access to CNV analysis services based on Agilent's platform and OGT’s quality control processes. Clough said, for example, that OGT's workflow now includes more than 30 "in-process QC checks applied to every sample and throughput in excess of 1,000 samples per week."

The company uses an in-house laboratory information-management system to record all equipment and reagents that are used throughout the protocol. Additional investments were made in robotics, automated-slide processing using SciGene equipment, and a large bank of hybridization ovens and scanners, he said. OGT's headcount has also risen 34 percent over the past year to include over 60 "expert employees, [a] significant proportion" of which are involved in array CGH, Clough said. The company employed 47 in January 2009.

OGT is also an Agilent certified service provider for processing samples for gene expression, miRNA, methylation and ChIP-on-chip. The company maintains separate lines of products for cytogenetic research and ChIP-on-chip studies, though those arrays are also manufactured by Agilent.