Oxford Gene Technology last week launched an array set for chromatin immunoprecipitation (ChIP)-on-chip studies of the K12 strain of Escherichia coli fulfilling its promise to bring microarrays to market.
Separately, the company said that the arrays it has developed for array comparative genomic hybridization applications will soon start alpha testing.
The K12 E. coli chip is the first product from OGT, which was originally set up to protect the patent estate of microarray pioneer Edwin Southern. It is also the first installment of what the company expects to be a prokaryotic microarray portfolio for ChIP-on-chip applications numbering in the "tens," according to a company official. A follow-up launch is planned for the third quarter, the company said.
James Clough, OGT's commercial director, told BioArray News this week that the firm decided to go with K12 for its first product because K12 is a non-pathogenic strain that is frequently used as a model organism.
The array was developed with Steven Busby of the University of Birmingham, UK, he said. Busby deferred all questions to Clough.
"We have been doing a lot of service projects in the prokaryotic area, both in gene expression and ChIP-on-chip," said Clough. "And this is part of the philosophy of the service business, which is, as we [perform services] we identify product opportunities. Since E. coli is the most studied prokaryotic organism, it was a natural starting point in terms of developing products for the prokaryotic range," he said.
"We'll continue to monitor the market and the needs of our customers before we make a decision on whether or not to add these arrays to our portfolio."
Clough said OGT sells the chip in a kit that contains three 60-mer arrays with 22,000 probes designed for ChIP-on-chip analysis of K12. The kit, which costs around £1,000 ($1,800) apiece, also includes cDNA and informatics designed in-house.
The informatics package, called ChIP Browser, enables users to "take the feature-extracted array data and then load it into [the software to] effectively compare that with the genome," Clough said. He added that all of the K12 arrays are printed using the firm's Ink Jet In Situ Synthesis method, which "jets down individual bases onto the array" in a manner "similar" to Agilent's ink jet printing capabilities, according to Clough.
"You don't need masks and you don't need to buy 22,000 oligos," he said of the IJISS printing method. This enables OGT to "address smaller market requirements in a more cost effective manner, because obviously the community for E. coli K12 is nowhere as big as the community looking at the human genome," he said.
Clough said OGT is now eyeing a midsummer release for a second array for ChIP-on-chip applications with probes for the pathogenic 0157 strain of E. coli.
He said that by releasing the E. coli arrays, OGT is focused on selling to niche research markets. Other organisms being considered for future chips are Salmonella and Mycobacteria, Clough said.
"We have identified that there is a significant opportunity in terms of prokaryotic ChIP-on-chip analysis," he explained. "Each prokaryotic organism has its own community. There are some that are studying model organisms but a significant number of prokaryotic researchers are looking at the pathogenic strains. So it's a combination of more academic science in terms of the model organisms but then there's a huge amount of research going on in understanding the pathogenic organisms," Clough said.
By targeting arrays for researchers doing ChIP-on-chip analysis of E. coli strains, OGT may have carved out a niche for itself in an overlooked market. While several companies already have arrays on the market for ChIP-on-chip studies, including Affymetrix, Agilent, and NimbleGen, only NimbleGen is currently offering E. coli chips as a catalog product for ChIP studies. NimbleGen spokesperson Joleen Rau told BioArray News last week the company also has a "full genome tiling for every prokaryote in GenBank."
Still, NimbleGen's offering differs from OGT's because all of its arrays are processed at NimbleGen's lab in Iceland, whereas OGT is selling an off-the-shelf product.
While Affymetrix does not have a catalog tiling array for E. coli ChIP-on-chip studies, spokesperson Andrew Noble last week said that the company "is currently working with customers on a number of custom model organism arrays, including E. coli."
Affy this year launched whole-genome tiling array products for five different organisms: human, mouse, Arabidopsis, S. cerevisiae, and S. pombe. Noble told BioArray News that the company intends to add C. elegans to that portfolio within the next two months. However, Affy has yet to commit to a catalog E. coli ChIP product. "We'll continue to monitor the market and the needs of our customers before we make a decision on whether or not to add these arrays to our portfolio," Noble said.
In a similar boat is Agilent Technologies. Spokesperson Stuart Matlow told BioArray News last week that the company is considering adding an E. coli array to its ChIP-on-chip portfolio. However, he declined to discuss a timeline for introducing that product.
OGT's Array CGH in Alpha Testing
One arena in which Agilent and OGT are sure to compete is the market for array comparative genomic hybridization chips. Agilent and NimbleGen have been offering their own oligonucletide arrays for array CGH since last year, and Clough said last week that OGT intends to market these chips for detecting constitutional changes.
"In terms of the constitutional arrays, we are internally testing the designs and we will [begin] alpha testing [them] in the summer," Clough said. We are very much intending to launch array CGH oligonucleotide arrays and we are targeting the constitutional disorder area. There's a lot of interest in using oligo arrays in this area," he added.
OGT has been collaborating with the Oxford Genetics Knowledge Park, a UK government-funded think tank, to develop array CGH tools for UK cytogeneticists to use in diagnosing patients with chromosomal abnormalities.
In February, Clough said that the firm's "overall direction [for array CGH] is the move into molecular diagnostics" (see BAN 2/14/2006).
"That's an area where we want to bring together a number of different things, and really, the Oxford GKP [partnership] is an example of that work," Clough said at the time.
— Justin Petrone ([email protected])