California start-up Prognosys Biosciences and German biotech Febit have begun jointly offering a service that combines next-generation microbial genome sequencing with functional gene-expression studies on custom microarrays, the companies said last week.
As part of the service, La Jolla, Calif.-based Prognosys will use Illumina’s Genome Analyzer to sequence genomes of bacteria for which no complete genome information is available.
Based on the sequence data, Febit, which is headquartered in Heidelberg and has an office in Boston, will custom-design microarrays for its Geniom One platform and offer to run array experiments as a service.
Its microarray platform can also help during the sequencing process by capturing and enriching parts of the genome for sequencing, and by verifying the genome assembly, according to Febit.
Customers can request the combined service from either company, and have the option to book the sequencing service separately from the array design, according to Peer Stähler, chief scientific officer of Febit. Prognosys is the key contact for setting up new projects.
Right now, the service is priced on a per-project basis as the companies are gaining experience with different types of microorganisms, but standard pricing packages will be available in a few months, he said.
Several potential customers have already approached the firms. Specifically, Prognosys is currently discussing three pilot projects with potential customers, two of them companies, according to Stähler. One of the projects involves sequencing multiple microbial genomes.
“Right now, we want to learn [from customers] what their needs are, and how fast we can address those needs,” he said.
Prognosys will use Illumina’s Genome Analyzer to sequence the microbes, but no further information was available regarding the pilot projects, the assembly and annotation strategies, and the experience the company has with the Illumina system. Prognosys CEO Mark Chee declined to be interviewed for this article.
The company’s website provides no background information about the firm but states that it is “developing innovative assay technologies” that it will make available “for applications ranging from basic research to clinical diagnostics,” and to “discover and validate molecular markers that have prognostic value.”
Prognosys was founded in 2004, and since 2005 it has won three grants from the National Human Genome Research Institute. These grants involve determining the targets of small molecules using a yeast-based haploinsufficiency profiling assay, applying microarrays to detect new cancer genes, and developing a low-cost oligonucleotide manufacturing process.
“In far less than a week, we can go from an annotated genome to hybridizing and creating data.”
According to Stähler, Febit’s microarray platform will help with the sequence assembly, verifying that the short sequence reads from Illumina’s platform were put in the right place. Specifically designed arrays “will check whether the physical DNA molecule that your sequencing approach tells you should be there really is there,” he said. “It’s kind of an empirical support … for the assembly of the final sequence.”
Following the sequencing, Febit will design a microarray for its platform, based on the genome. It also offers to build the array on its Geniom One instrument, and to run gene-expression studies as a service. Alternatively, customers who own a Geniom One can build their own arrays and run functional analyses in house. Designing and building a microarray is quick once the genome sequence is available. “In far less than a week, we can go from an annotated genome to hybridizing and creating data,” Stähler said.
The service, he suggested, will appeal to researchers who want to use microarrays to characterize yet-unsequenced microorganisms, such as pathogens or production strains, but don’t want to bring new sequencing technologies in-house. Though scientists have the option to book the sequencing service separately from the array design, the combination is what makes the service unique, he said.
Another advantage Prognosys has is its CEO’s experience with arrays. Before founding Prognosys, Chee worked for Affymetrix in the 1990s and co-founded Illumina in 1998.
“Other companies, they might be good at sequencing, but if they don’t understand microarrays, you have a much higher barrier, [and] you have a potential loss of speed, because the handover of projects, the creation of a data pipeline, is much more difficult,” Stähler said.
In the future, Prognosys and Febit might broaden the service to include larger genomes. “I think we would not be prepared for a eukaryotic genome immediately, but we might be soon,” Stähler said. “It depends, really, on the progress of the current projects.”
For bigger genomes, Febit’s microarrays could also be used to capture parts of the genome and prepare them for sequencing, Stähler said. The company has been working independently on this application of its technology, which it plans to make commercially available next year.