German array firm Febit has partnered with California start-up Prognosys Biosciences to launch a service that combines next-generation sequencing and on-the-fly array design in order to create custom microarrays for the microbial genomics community. The service, which first sequences the genome of a microbe of interest and then places it on arrays, is expected to save researchers money and show off the flexibility of both sequencing and array technology, according to the partners.
According to Febit CEO Cord Stähler, the companies’ Genome-to-Array service should become a catalog offering through Febit by early next year. “We are prepared to take first projects right away and foresee the service to be a standardized process within six months,” he wrote in an e-mail to BioArray News this week.
Stähler wrote that customers will request the service either through Prognosys, whose lab is equipped with an Illumina Genome Analyzer, or Febit. Prognosys will sequence the organism of interest and deliver the data to Febit, which will generate arrays using its Geniom One instrument. The partners figure that between the speed of the service, which takes on the order of weeks, and the ability to make novel microbial genomes available on low-cost microarrays, they could be offering a profitable service to the market.
“The opportunity is unique because of the deep knowledge involved in performing this type of work in a short period of time,” Stähler wrote. Febit and Prognosys will be able to go “from biological genetic material to a working microarray experiment in weeks,” he wrote. “This has mainly to do with the deep understanding of how genetic assays function and can best be made to work,” he added.
According to Stähler, another asset is the know-how of Prognosys CEO Marc Chee, who served as a scientist at Affymetrix in the 1990s prior to co-founding Illumina in 1998 where he held several positions before leaving to found Prognosys in 2004. In fact, the Genome-to-Array service grew out of Febit’s relationship with Prognosys, which has both a Genome Analyzer and a Geniom in its lab in La Jolla, Calif.
Chee told BioArray News last week that the concept behind the service was to reach customers that are not served by the current generation of whole-genome arrays on the market.
“If you study the human genome or rat or mouse, your needs are pretty well met by standard arrays sold by companies like Illumina,” Chee said. “At the same time, the field is developing very rapidly with the introduction of new sequencing technology and a lot of people want to study organisms where there are not great standard sequences, let alone great arrays,” he added.
Chee said that the service could exploit a “potentially big niche” by enabling researchers to get from a sample of DNA to arrays. He also said that the service is “more for people that are interested in exploring organisms that are not well mapped,” especially microbial genomes.
According to Chee, the work will also help buoy Prognosys’ development plans. “We have a Geniom and a Genome Analyzer and we have the capabilities to do this work. We also thought this would be a good way to generate revenue to support some of our other activities,” he said.
Chee declined to discuss what kind of technology Prognosys is developing. The company has received roughly $1.3 million in Small Business Innovation Research grants from the National Institutes of Health since 2005. Project titles include, “Microarray Technology for Genomic Assays”, “An Assay System for Cancer Gene Discovery”, and “A Highly Parallel and Sensitive Assay System for Chemical Genomics.” In addition to SBIR grants, Chee said the firm is backed by an undisclosed amount of private equity funding.
Febit’s and Prognosys’ service is new but the concept behind it is not. Technically, any scientist with access to a sequencer, some heavy-duty bioinformatics resources, and an arrayer could do exactly what the two firms are offering. However, both Stähler and Chee pointed out that the costs for sequencing a microbe – roughly $100,000 on the Genome Analyzer — plus the resources put into designing an array have held scientists back from doing just that since next-generation sequencing became available.
Instead, they are betting that their pooled resources and expertise make them the more cost-effective option for their target market. “For most labs, doing this on their own would not be cost effective,” said Chee. “On the order of microbial genomes, we can make it accessible to small labs, biotech companies, and people who have an interest in organisms that are possibly still using cDNA arrays and things like that,” he said.
“A lot of people want to study organisms where there are not great standard sequences, let alone great arrays.”
“In general, researchers can perform the process themselves, but it will cost them much more and take much longer, if they can get the broad spectrum of related skills together,” said Febit’s Stähler. He declined to provide exact pricing for the service, but said that the two will charge “standard pricing” for the Solexa sequencing, the Geniom array platform, and the bioinformatics work.
“The price will be calculated on a case-by-case basis and can be on an effort base or a fixed price for a given target,” said Stähler. “The de novo sequencing of a small genome all the way to a validated Geniom array can be performed in weeks.”
According to Stähler, the workflow of the service will also be decided on a case-by-case business. The Geniom array design could take place in La Jolla or at Febit’s US office in Boston. Bioinformatics work will be handled in Boston where the firm’s vice president of bioinformatics, Anthony Caruso, is located.
Over the past year, Febit’s business model has changed from one based mostly on services to one that also relies on sales of consumables. The evolution in strategy culminated this year in the launch of its Geniom Analyzer instrument, a lower-cost instrument that is priced at about half of the Geniom One at $100,000 (see BAN 3/13/2007).
Unlike the Geniom One, the Geniom Analyzer is a benchtop system that cannot synthesize arrays. However, Febit believes the Analyzer is ideal for researchers that would like access to its arrays, but cannot afford or do not need the functionality of the Geniom One.
Stähler said that it is technically possible for customers of the Genome-to-Array service to migrate the content to another platform. However, he said that they would most likely stick to using the Geniom because of cost factors.
“The sequence information will be transferred into a digital array that can immediately be synthesized and analyzed on the Geniom,” he said. “Once the assay and especially the capture probes are validated, the assay could in principal be transferred to a different platform, but that will require new validation so it is unlikely to happen as Geniom is price competitive,” he said.