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Nebion, Qlucore Partner to Provide Complementary Capabilities to Customers

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Swiss bioinformatics firm Nebion and Swedish bioinformatics company Qlucore have agreed to jointly promote their flagship products, thereby offering a complementary set of capabilities for the pharmaceutical and biotechnology industries that can be used for biomarker discovery studies and more.

Qlucore’s Omics Explorer software lets researchers analyze and identify patterns in high-dimensional data from microarray experiments. Nebion, for its part, provides well curated data culled from public resources through its Genevestigator, a platform that integrates gene expression data with annotations. Genevestigator is complementary to Qlucore’s offering because it enables "web-based systematic screening of genes across many thousand experiments," Carl-Johan Ivarsson, Qlucore’s CEO, said in a statement.

Elaborating on why both companies see their products as a good fit, Nebion CEO Philip Zimmermann explained that while Qlucore’s software supports in-depth analysis of samples in single experiments, his firm’s database offers access to a much wider pool of experimental results making it possible to explore findings from single studies in the context of a much larger body of research data. Conversely, customers who pay for the right to use the Genevestigator can pull information from its database and use Omics Explorer to analyze it.

Nebion’s Genevestigator is made up of a search engine and a curated database of primarily human, mouse, and rat gene expression data from microarrays, and RNA sequencing data pulled from public resources such as the Gene Expression Ominibus and Array Express. It has the ability to simultaneously run through data from tens of thousands of microarrays providing rapid results.

Genevestigator uses controlled vocabularies to consistently capture information about experiments and sample descriptions such as clinical and patient characteristics from the public domain. It provides summaries of gene expression across tissues, cell cultures, cell lines, cancers, diseases, drugs, chemicals, hormones, or genotypes, which could help drug companies, for example, make decisions about the effectiveness of potential drug targets. By the same token, access to this information could help drug companies identify genes that are uniquely expressed in disease conditions of interest to them that might make good treatment targets.

Initially, Genevestigator was an academic program run by researchers at the Swiss Federal Institute of Technology (ETH) in Zurich. When it began in 2003 as a plant-specific project, its objective was to create standardized datasets for the Arabidopsis community. Following the success of this first resource, the researchers in charge also began generating non-plant content. They started by adding mouse data to the database in 2006, and in 2008 they moved on to human data. This was also the year when the team spun off from ETH Zurich to form Nebion and licensed the Genevestigator technology from the institution, Zimmermann told BioInform.

The Genevestigator database still contains plant information — and there is also some data from microorganisms — but the "main drivers" for the company now are its human, mouse, and rat datasets, Zimmermann said, and Nebion plans to keep adding content for its existing organisms, especially for humans. That includes adding SNP chip and DNA data, for example, but also focusing on collecting disease-pertinent information. This is the approach used by competing companies such as Compendia Biosciences — now owned by Life Technologies — whose Oncomine database covers cancer genomics in great depth, and MediSapiens, which also provides curated oncology data as part of its OncoGenomics Explorer application.

Right now, Genevestigator has general information on about 170 diseases and since it’s not feasible to focus on every single one of those conditions, Nebion has had to select a subset of conditions to cover in greater detail, Zimmermann said. That list includes respiratory, cardiovascular, and autoimmune diseases, dermatology, ophthalmology, and neurology. It also covers cancer to some extent but not as a primary focus. Subject to customer demand — and depending on the availability of public data — the company will also consider expanding the number of organisms it covers, he added.

Current customers include Novartis, Roche, Nestle, BASF Plant Science, Syngenta, and others. Pricing for annual licenses to Genevestigator varies depending on which version of the product customers select. The cheaper option is to access the system online. Alternatively, customers can have a local version installed behind their firewalls. The second option affords those who choose it the ability to combine private and public data. They also get help with curating their proprietary data with the same approach used in Genevestigator, Zimmermann said. The company does not make its fees public.

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