Oxford Gene Technology last week expanded its offerings for bacterial research with the launch of its Universal Prokaryotic high-density oligonucleotide arrays for use in chromatin immunoprecipitation-on-chip, gene-expression, and comparative genomic-hybridization experiments.
The microarrays are manufactured by Agilent Technologies and feature multiple arrays per slide. The company said it developed the arrays in collaboration with the prokaryotic research community, and arrays are available for Escherichia coli, Salmonella typhimurium, Streptomyces coelicolor, and Mycobacterium tuberculosis, among other organisms.
The new array offering extends the Chip² arrays OGT launched in 2006 for prokaryotic ChIP-on-chip research by adding gene expression and CGH applications to the same slide (see BAN 5/30/2006). The launch is also the result of an agreement that OGT signed with Agilent in 2007 under which Agilent became an original equipment manufacturer for OGT-designed catalog microarrays, and OGT became an.Agilent certified service provider (see BAN 1/16/2007).
An OGT official said the decision to make chips available for both gene expression and CGH in prokaryotic studies was made to meet customer demand and to take full advantage of Agilent’s manufacturing capabilities.
“We have been working with a number of prokaryotic researchers and had developed the Chip² arrays, but they were just genomic arrays and we had a separate set of designs for gene expression,” Marcus Harrison, product manager at OGT, told BioArray News this week.
“We thought it was a good idea to cover both genomic applications and gene expression on the same slide,” said Harrison. “The majority of our products are about 44,000 probes and on our 4 X 44K array format, we have customers that have hybridized two gene expression experiments on one half of the array and two ChIP experiments on other half,” he said. “So that’s a very cost-effective solution.”
According to James Clough, OGT’s commercial director, the company began targeting the prokaryotic research community before it signed the Agilent pact, when the density limit for its arrays was about 22,000 probes — too small for a human or a mouse genome, but just right for communities of researchers that had been spotting their own whole-genome arrays to look at prokaryotic organisms like E. coli or S. typhimurium.
“A lot of the groups weren’t served by big array suppliers,” Clough told BioArray News this week. “Historically, volume has been in human, mouse, and rat. Until both OGT and others began working in this area, the groups have made their own arrays because the volume is smaller,” he said.
Clough said that recently two trends have favored OGT’s business strategy. The first is the increasing availability of second-generation sequencers that are constantly producing new genomic data that, in turn, leads prokaryotic researchers to redesign their arrays. The second is the narrowing of the market for spotting instruments, which makes commercial chips a more viable option for budget-constrained academics.
“What has been fascinating is that we have been developing the prokaryotic range with leading researchers around the world, and that group historically has almost exclusively been spotting,” said Clough. “They usually work in a consortium to design oligos and then someone makes them. The challenge that those groups have had is the sequence keeps evolving because, with next-generation sequencing, more strains are being sequenced and there is a better understanding of prokaryotic genomes.”
“This is the next step forward from Chip², where we are broadening the range of applications that you can do on a slide.”
The relatively quick turnaround offered by OGT leverages Agilent’s inkjet in situ synthesis manufacturing capabilities plus its multipack array formats, where the company can print two, four, or eight arrays on a single slide. All chips are manufactured at Agilent headquarters in Santa Clara, Calif., and then provided to OGT customers through its services lab in Oxford or as a catalog product.
Customers can use OGT’s internally developed ChIP Browser software for ChIP studies or seek advice from the company for expression or CGH analysis tools. Pricing will be “competitive with market price,” Clough said, but “each project has its own nuance in terms of design challenge and the number arrays people are looking to use.”
“What is happening is that a lot more strains are being sequenced and people are saying, ‘We’ve got this one sequence and we want to add it on’,” said Clough. “In the past, they would have had to start fresh with an oligo set. Now, we change our design, change our file design, and print a new array.”
Clough added that second-generation sequencing is just beginning to have an impact on OGT’s business, and that this preliminary trend could grow in coming months as more instruments that have been placed become functional. “Not all of those instruments are up and running at capacity,” he said. “I think it is going to change quite quickly, and I think that is why a lot of groups have decided not to make in-house arrays, but to buy a commercial product.”
Another factor that may be pushing users in OGT’s direction is the thinning out of the market for array spotters. While higher-throughput spotters, such as those sold by Arrayjet and Aushon Biosystems, are flourishing, primarily due to an energized protein array market, smaller, do-it-yourself systems are harder to find, Clough said.
“Five or six years ago there were a lot of companies in spotter business, but the choice is reduced now,” he said. “A lot of people have also realized that, in the past, if you had a core, you were at the forefront,” he said. “Now people realize that making arrays is not as interesting as it once was. To reliably make spotted oligo arrays is quite a challenge. The funding bodies are also saying that you can now buy a commercial array instead,” he said.
The target customers for OGT’s latest offering are typically researchers or consortia of researchers studying a particular prokaryote. For example, Colin Smith, professor of functional genomics at the University of Surrey in the UK, helped develop a Streptomyces coelicolor high-density array for use by the Streptomyces coelicolor Microarray Resource, which is manufactured by OGT and supported with funding from the UK’s Biotechnology and Biological Sciences Research Council and the EU’s Framework Program 6 ActinoGEN program.
Smith said in a statement last week that “advanced printing technology cost-effectively produces high-density arrays with a quality that is far superior to spotted arrays.” He did not respond to an e-mail seeking further comment by time of publication.
According to OGT, other Universal Prokaryotic array users include Joseph Wade of Harvard University and Dave Grainger and Steve Busby at the University of Birmingham, who are focused on E. coli; Jason Hinds from the Bacterial Microarray Group at St. George's, University of London, who is producing a range of prokaryotic pathogen arrays; and Peter McGlynn at the University of Aberdeen, who is also studying E. coli.
Clough said that the latest offering from OGT builds on a corporate strategy of turning research collaborations into catalog products. “Most of our products are the result of an initial service project,” he said. “We have done a service project and we have generated a product.”
From a broader perspective, he envisions that customers in both the agricultural biotechnology space as well as those studying drug resistance will begin to adopt OGT’s platform.
“In terms of customer base we have got organisms that are an agro-economic cost; they cause disease in livestock,” he said. “Over the last 10 years there’s been ever more press coverage about the problems of disease resistance. With the sequencing that is taking place, you can now make an array to look at a whole range of pathogenic organisms.”