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Pocketing $3.7M, Eureka Touts Informatics as Differentiator in Sequencing Services, Microorganism Detection

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By Bernadette Toner

Fresh from a $3.7 million financing round, Eureka Genomics is looking to build out both sides of its two-pronged business model, which involves sequencing services as well as internal discovery projects to identify novel microorganisms associated with disease.

Underlying this hybrid model is a portfolio of proprietary bioinformatics tools that the company licensed in 2007 from the University of Houston.

Heather Koshinsky, chief scientific officer and co-founder of Eureka Genomics, told BioInform that the company's bioinformatics methods are "key" to its microorganism discovery efforts as well as its services business. "The bioinformatics tools allow us to have a fairly sophisticated service business that is along the lines of many companies' services businesses, with mapping and assembly, but it then allows us to take the next step and look for the unknown, as opposed to concentrating on the known," she said.

In particular, Koshinsky said that the company's algorithms do not rely on heuristics as do many bioinformatics tools like Blast. The algorithms, developed by Yuriy Fofanov, chief technology officer and co-founder of Eureka and director of the bioinformatics lab at the University of Houston, identify all subsequences present in any sequenced genome, as well as all subsequences with any given combination of mismatches. This allows the firm to distinguish potential genomic signatures from background sequence, according to company literature.

"It's a non-heuristic model, and because it's non-heuristic it eliminates approximations," Koshinsky said. "When you really need to understand exactly what the difference is [between sequences] and be able to use all the sequence data, you need to move to a non-heuristic model, and that's what these algorithms do."

The company also relies heavily on an extensive database that includes the complete genomes of 500 bacteria, 100,000 viruses, and several dozen host genomes including human. In addition, the database holds multiple reference sequences for many organisms, including more than 800 different strains of HIV and more than 60,000 strains of flu virus.

Using these tools in combination with high-throughout sequencing, the company is able to "approach the identification of microbial causes of diseases without needing to rely on the traditional tools to identify them," such as immunology, culture, and microscopy, Koshinsky said.

"Based on the presence of the nucleic acid in the disease sample, and the decreased presence of those same nucleic acid sequences in the asymptomatic samples, we get a handle on [a potential] biomarker associated with that disease, and that then moves us down the full discovery path that leads to programs in diagnostics, therapeutics, and vaccine development," she said.

The company is currently focused on cancer, with a lead project in colorectal cancer. Eureka is also looking at cardiovascular disease, "although those are just the first in the queue," she said.

Koshinsky cited several "very well characterized examples" of cases where previously unknown microorganisms were shown to be associated with disease, such as the link between human papillomavirus and cervical cancer.

Truly novel microorganisms pose a challenge in discovery, however, because they are dissimilar to known organisms and are therefore undetectable via homology-based approaches, microarrays, and 16S ribosomal DNA analysis. Eureka's ability to unearth these "unknowns" in the sequence data will give the company an edge, Koshinsky said.

Didier Perez, chief operating officer and co-founder of Eureka, said that the company is currently focusing on three undisclosed novel microorganisms, and that it has a total of 20 in its pipeline. Eureka plans to eventually partner with diagnostic firms and drug and vaccine developers to move these sequences downstream, "but we're not there yet," he said. "This will be the year where we'll start to discuss with potential partners how to best use those sequences that we've identified."

On the services side of the business, the firm plans to add to its single Illumina Genome Analyzer, which it installed in its Hercules, Calif., facility last April.

"We have not scaled up yet, but we clearly will have to this year because we are very close to capacity," Perez said. The company plans to use its new funding to acquire two more sequencers, but hasn't yet decided on whether to stick with the GA or move to another platform.

"The market will dictate to us what is the best platform," Perez said. "We'll buy whatever does the job, and we're starting to realize that for specific jobs some equipment may be better than others, and depending on how the service business develops and what the requests are, we may continue with just Genome Analyzers or we may add other types of equipment."

So far, Eureka has signed multi-year service contracts with two undisclosed national labs, and has also performed work for diagnostic companies, research companies, and universities, Perez said. "We're getting on average anywhere between five to seven requests per week, and from all over the world, for our services."

The company currently employs 10 staffers and has plans to use some of its new financing for new hires. Perez declined to provide details on the firm's hiring plans, but said that the company has brought in a new director of sales, Karen Roberts, who will focus on the service business.

Eureka is also looking to replicate its model in various spots around the world. Perez said that the firm is in discussions with groups in Southeast Asia and in Europe to set up a "network" of local sequencing centers "where we would apply our bioinformatics."

Perez said that the company expects to set up between six and 10 such centers over the next two years and noted that the funding "is a good step toward doing that."

While the firm is joining a list of sequencing service providers that includes SeqWright, Beckman Coulter Genomics, Complete Genomics, and others, Perez said that Eureka offers superior capabilities in experimental design and sample prep.

"Anyone can buy a sequencer, but if you have someone who really knows how to prepare the samples and someone who can design the experiments, this is where the value is added," he said. "And of course, because we're able to provide bioinformatics services that we know no one can do as we do, that also makes a difference."

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