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Genome Designs Seeks to Tackle Challenges of Functional Genome Annotation in NGS Era

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By Uduak Grace Thomas

Genome Designs, a bioinformatics services startup, has received an undisclosed amount of seed financing from private investors that it will use to support marketing activities and make improvements to its software tools.

The company, which officially opened its doors in January, offers manual functional genome annotation services based on a proprietary analysis pipeline developed by the company's founders, who include veterans from Argonne National Laboratory, the National Center for Biotechnology Information, Integrated Genomics, and Ariadne Genomics.

Genome Designs sees an opportunity for painstaking functional genome annotation amid the rapid rise of next-generation sequencing. The recent surge of sequencing projects has led to an increase in automatic genome annotation, which "causes errors from fused or frame-shifted ORFs to propagate and accumulate in the databases," Evgeni Selkov, chief scientific officer, said in a statement.

Such errors can result in Blast results "filled with perfect matches among 'putative uncharacterized proteins,'" he added.

In addition to functional annotation, Genome Designs uses its analysis tools to provide metabolic pathway reconstruction and engineering services. It plans to eventually out-license metabolic designs that would be of interest to pharmaceutical companies developing antimicrobial drugs or food and bioproduction companies seeking improved production strains.

The company's proprietary analysis pipeline, called the Genome Designs Annotation Suite, reconstructs core metabolic pathways and regulation mechanisms for newly sequenced organisms. It relies heavily on the Metabolic Pathway database, a collection of curated metabolic pathways co-developed by Selkov.

The repository currently contains more than 9,600 diagrams representing variants of metabolic and membrane transport networks of microorganisms, higher plants, and animals, including human, rat, and mouse genomes. It includes information on initial substrates, end products, coenzymes, and intracellular localization, among other details.

Genome Designs is currently seeking industry and academic collaborators. On the academic side, it is looking to work with government-funded groups who need assistance annotating newly sequenced bacteria, fungi, and plants.

The company is also looking to partner with groups who can experimentally validate its in silico metabolic designs. Such collaborators would share any intellectual property that would result from the partnership, CEO Natalia Alexandrova told BioInform.

Furthermore, Genome Designs plans to publish complete functional annotations for a number of genomes, which the company hopes can be used as a new "gold standard" for genome annotation, Selkov said.

The company will initially post annotations of two bacterial genomes, followed by additional annotated microbial genomes at a later date, Alexandrova told BioInform. She added that these collections will be freely available on the company's website as well as through relevant publicly available databases.

She also said that the company is working on improving human tissue-specific pathway collections that are included in the MPW database. While it will provide services based these data, it might also make the information available for free on its website, she said, adding that the process could take several months.

While Genome Designs is currently relying on a services model, it is considering making parts of its internal pipeline publicly available at a later date, Alexandrova said. The company is also working with an undisclosed partner to develop tools that could be available as early as the end of February, although the partners haven’t decided yet if the software will be free.

Building a Business

The company intends to focus on functional reconstructions of the molecular physiology of organisms, as well as metabolic modeling for customers, Alexandrova said.

These capabilities would be useful for clients looking to create improved strains of bacteria for use in biofuel production, or for pharmaceutical companies trying to design treatments for bacterial infections, she said.

The four-person company hopes to woo researchers in bioproduction, food, and pharmaceutical companies as well as academic institutions that are looking for bioinformatics solutions that don’t require software licenses, Alexandrova said.

She added that a second category of potential customers would be biologists who don't want to become bioinformatics experts but simply want to run the necessary analysis pipelines to get the results they need.

Alexandrova said that Genome Designs' services-oriented business model sets it apart from companies like Integrated Genomics and Ariadne, which sell software products for metabolic engineering and pathway analysis, respectively.

Integrated Genomics does offer some microbial metabolic engineering services that compete with Genome Designs' offering; however, this isn't an issue for Alexandrova.

She explained that given the "service model of our business" a small company like Genome Designs would only be able to take on a few number of clients at a time.

As a result, "the more companies like ours are out there at this particular time, the better for the industry," she said.

At present, Genome Designs has some potential customers in its sights including an academic institution, a biofuel company, and an RNAi-based company, Alexandrova said, although she could not go into more detail since service agreements with these groups have not yet been signed.

Although the cost and timeframe of its services are determined by the nature of the project, to completely annotate and reconstruct the metabolic pathway of a microbial genome would cost somewhere in the vicinity of $50,000 and take two to three months to complete, Alexandrova said.

Genome Designs is headquartered in Walnut Creek, Calif., and has offices in Naperville, Ill., and Moscow.


Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com.

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