Capping off two years of roundtables and collaborations, Oxford Gene Technology next month will make its first foray into the market for catalog arrays for comparative genomic applications by launching two chips tailored to meet the growing needs of the global cytogenetics community, according to a company official.
OGT R&D Director John Anson told BioArray News this week that the UK firm will begin selling its CytoSure Chromosome X Array and its CytoSure Syndrome Plus Array at the European Cytogenetics Association Conference in Istanbul early next month.
Both products bear the CytoSure brand, which has been created to cover all of OGT’s future cytogenetics-related product launches. They are being sold for research use only, although the company said that diagnostics — including CE Marking in Europe and a 510(k) route to clinical use in the US — could be in their long-term future.
Moreover, they underscore the attention OGT is giving the cytogenetics research community. “We feel that we have the only oligo arrays designed exclusively for the cytogenetics community,” Anson said. “We have taken our own in-house designs and designed these arrays to directly focus the interest we are getting from that community.”
According to Anson, the Chromosome X Array arose from a collaboration with Phillipos Patsalis, chief executive and medical director at The Cyprus Institute of Neurology and Genetics in Nicosia, Cyprus.
“He had an idea of what would make a good array, we agreed, and we basically designed an exon-specific array, a high-density array with 44,000 features all focused on the X chromosome,” Anson said.
Patsalis’ lab in Nicosia finished alpha trials on the product several moths ago and OGT said it has used its own samples for beta trials. While the Chromosome X Array was originally designed for Patsalis’ group, Anson said that OGT has seen “quite a lot of interest in the X chromosome product” because “there's very little like it on the market.”
There are a number of disabilities associated with the X chromosome, including Duchenne muscular dystrophy and hemophilia and "a lot of research has been done on mapping those abnormalities effectively,” Anson said. “Of all the 23 pairs of chromosome, it is the one that has the highest density of interesting areas associated with learning disabilities.”
Patsalis could not be reached for comment.
With wider coverage than the Chromosome X Array, OGT’s CytoSure Syndrome Plus array took root two years ago — a time when OGT was retooling itself from being solely an IP licensing firm to one that also sold products and services. However, the real driver behind the launch of Syndrome Plus was a cooperative agreement signed with Agilent Technologies earlier this year (see BAN 1/16/2007).
Under the terms of that agreement, OGT gained access to Agilent’s microarray platform and appointed Agilent as an original equipment manufacturer for OGT-designed catalog microarrays, while Agilent certified OGT as a provider of services based on its array platform.
“Syndrome Plus kicked off from a roundtable we had in the summer 2005, but our array density was limited to 22,000 features at the time,” Anson said. “More recently we signed an agreement with Agilent that gives us access to greater density formats and gives us the opportunity to make an array with a much greater density of features.”
Based on those higher-density capabilities, the Syndrome Plus array covers 85 distinct genetic syndromes — including Cri du Chat, diGeorge, Downs, and Prader-Willi — in two, 105,000-feature arrays printed on one slide. Anson said the duplex format will enable users to “either run two samples on one color or do a single sample with a dye swap on one array.”
While not a tiling array per se, OGT’s Syndrome Plus chip offers genome-wide coverage, albeit at varying resolution. “We have really targeted the hot spots for the cyto community,” Anson said. “What we have also done is been able to put landmark probes across the genome, to give kilobase resolution in areas where there are known abnormalities, lower in areas where there are no known abnormalities,” he said. “We haven’t tiled across the genome in an equal way, we've biased it towards areas of interests in the genome,” he added.
“These are for RUO now, but we will look at the potential for CE marking in Europe and perhaps US Food and Drug Administration approval in the future.”
When customers order the arrays they will also receive OGT-designed CytoSure visualization software, a tool “based around the latest build of the human genome sequence” that also incorporates copy number variation data from recent studies. OGT has not disclosed pricing for the arrays.
A key factor in user adoption will be OGT’s decision to use oligonucleotides — considered too noisy by some for diagnostics — rather than bacterial artificial chromosomes, which are less amenable to the large-scale manufacturing necessary in a consumables-driven business.
Both CombiMatrix Molecular Diagnostics and Signature Genomic Laboratories have dismissed the idea of using oligos in their labs, although Baylor College of Medicine recently broke with the pack and said it will use an oligo platform manufactured by Agilent Technologies in its chromosomal microarray analysis testing services (see BAN 4/3/2007).
Anson said that OGT believes the market can accommodate both technologies. “What is good about having both BACs and oligos is that customers are getting a choice. Oligos offer greater probe density and greater security and confidence in the data,” he said. “So you are not just looking at a few data points, we are generating many data points associated with a certain syndrome. It is really helping to build confidence and security in being able to make decisions based on the content on the arrays,” he added.
OGT’s new chips will be sold for research only, but Anson conceded it is possible for cytogeneticists to use them as preliminary screening tools that can be followed up with existing cytogenetic tests such as fluorescent in situ hybridization. Beyond that, though, lies the prospect for genuine diagnostics. So far, OGT has expressed interest in pursuing a diagnostics route, but little more.
“These are for RUO now, but we will look at the potential for CE marking in Europe and perhaps US Food and Drug Administration approval in the future,” Anson said. “We will have to look at how things are developing and work with regulators as well. It is a new tech but it is something that we are following closely.”
In the meantime, OGT will reach out to customers in its home UK market like the Wellcome Trust Sanger Institute and various regional centers to spur adoption of the technology while it looks to attract users in other key markets like North America and Japan. According to Anson, there is a real potential for CGH chips like Syndrome Plus to become the first arrays to become widely used by clinicians.
“Cytogeneticists are getting more experienced with handling arrays and they are the people who are effectively in the front line [and] dealing with pediatricians and families,” he said. “They also want to feel more in control of the tools they are using. Cytogeneticists can use this breakthrough technology in conjunction with other more conventional technologies they have at their disposal and pass on the benefits to the pediatricians and patients,” he added.