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GenomOncology Emerges from Stealth Mode with Products for Cancer Research, Clinical Applications

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After operating in stealth mode for the better part of the last two years, GenomOncology is now broadly marketing two proprietary software solutions that it has developed for managing and interpreting oncology data in clinical and research contexts.

The company's GenomAnalytics platform provides a step-by-step workflow for analyzing and interpreting large cancer datasets. It includes tools for checking the QC metrics of sequencing runs and samples and retrieving raw sequence files from sequencing instruments to check for errors at the base pair level, as well as capabilities for exploring the effects of SNPs, structural and copy number variation, and loss of heterozygosity regions on genes and pathways. There are also customizable templates for creating reports, and the company includes copy of the public TCGA data with its installations.

Its GO Clinical Workbench has many of the same capabilities that the research product does but its workflow is tailored towards analyzing and reporting on tumor variants in clinical cases. Included in the decision support software are a series of interfaces through which members of clinical labs interact with the data. Through one interface, lab managers can check quality of runs and samples; a second screen lets a genomic analyst validate, classify, and annotate called variants and draft reports that are passed on to the pathologist for review and approval — via a third interface — before the results are sent to the requesting oncologist.

Both solutions can be integrated with onsite infrastructure such as Illumina and Ion Torrent instruments, laboratory information management systems, and electronic medical records. Default quality control and annotation parameters in both systems as well as report templates can also be changed depending on clients' needs. For example, a final clinical report used by one lab might include information about variants and ongoing clinical trials, while another lab might just want to list variants and possible treatment options.

Pricing for the GenomAnalytics platform varies depending on the institution and its particular research needs. In terms of its clinical product, users are charged for the cost of the software installation and integration with any existing systems — the specific cost is not disclosed — and then some customers pay the company a portion of the revenue they earn from every genome they analyze using the company's software, President and CEO Manuel Glynias, told BioInform. Another option for customers of its clinical solution, he said, is to pay the company a percentage of the reimbursements they receive from analyzing genomic data from patients. The company is not disclosing the exact fraction of the reimbursement it intends to collect from clients who select this payment plan. It’s a small enough percentage that the labs are able to turn a profit, Glynias said, "but it's significant enough … that we think we can make a reasonable living on it."

The company's products are already being used in places such as the University of Pittsburgh's biomedical informatics department, for example, where researchers are using GenomAnalytics to explore, mine, and interpret data from the Cancer Genome Atlas as part of a personalized medicine research initiative. Also, CompanionDx, a commercial CLIA lab specializing in pharmacogenetics, cancer companion diagnostics, and more, has selected the company's clinical workbench solution to manage its genetic testing workflow and to generate the reports it returns to requesting physicians.

Glynias said that the company is "actively negotiating" contracts with new customers and it hopes to drum up interest in its solution at scientific meetings such as the annual Advances in Genome Biology and Technology conference — being held this week in Florida — and at the United States & Canadian Academy of Pathology meeting in March.

Cleveland-based GenomOncology has spent the nearly two years since it was founded in May 2012 developing and testing versions of its research product at places such as Cleveland Clinic's Genomic Medicine Institute and thinking through an effective commercialization strategy that includes a pricing scheme that’s rather unusual in the bioinformatics arena. Much like many other informatics companies, their goal was to develop software solutions that enabled customers who prefer to do their own analysis — mainly for privacy reasons — to do so, and at the same time provide an easy-to-use intuitive solution for labs without in-house informatics experts. "We thought really hard about the kinds of queries people want to do against cancer genomics data and then thought about what would be the right way to represent that data so that it would be easy to query against it in a flexible way," Glynias told BioInform.

The company's initial strategy was to establish a presence in the bioinformatics market by developing and selling its research application, Glynias said. It planned to begin offering clinical applications for cancer genomics after three to five years of building up a strong customer base among cancer research centers. Delaying the release of the clinical product would give the company time to study the unique requirements of the arena and to tailor its solution to meet those needs when that market eventually took off. But the shift towards clinical applications of NGS happened much faster than GenomOncology anticipated, causing it to move up development plans for its clinical product, Glynias said.

That led to collaborations with both Roswell Park Cancer Institute (RPCI) and the Vanderbilt-Ingram Cancer Center on the development of the GO Clinical Workbench. In addition to an ongoing collaboration with RCPI that began last June to develop and refine the software, GenomOncology has signed an agreement with Vanderbilt that makes it the exclusive commercial licensee of the latter's My Cancer Genome, an online data repository of curated information a total of 18 cancer types including breast, bladder, colorectal, ovarian, and thyroid cancers, as well as curated information about 26 genes and variants within those genes that are targeted by therapies. GenomOncology's products use information from this database to help users classify and prioritize mutations by tumor type, for example. It is also the source of the in-depth information on mutated genes, pathways affected by these mutations, clinical trials, and possible treatment suggestions that customers can include in reports.

Under the terms of the agreement, Vanderbilt will receive a portion of the fees — the exact amount is not being disclosed —that GenomOncology charges per sample analyzed as a royalty for the company's use of the My Cancer Genome database, Glynias said. This arrangement does not affect the free use of the database for non-commercial purposes but commercial companies wanting to use My Cancer Genome from now on will have to buy their licenses from GenomOncology. The company is also working with Vanderbilt on some improvements to the resource, Glynias said. For example, it is incorporating tools that will make data curation faster and features that will make it possible to curate more "complicated" sorts of data.

Meanwhile, GenomOncology has received an undisclosed amount of venture capital from TriStar Technology Ventures in a deal that includes a seat on GenomOncology's board of directors filled by John Doulis, chief information officer of TriStar's partner fund, MedCare Investment Funds. Previously, it raised an undisclosed amount of funding from local Ohio investors which it is using to bring its products to market. The combined funding from its investors is enough for the 14-person company to run its business for the next year or two, Glynias said.

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