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Spiral Raises $3M in Financing, Pursues Partnerships to Tap into Clinical Genomics Analysis Market


Bioinformatics software startup Spiral Genetics has raised $3 million in series A financing and signed a partnership with genome interpretation firm Omicia in a bid to reach customers in the clinical genomics analysis market.

The deal with Omicia is the first of several partnerships that Seattle, Wash.-based Spiral Genetics is planning in order to offer variant interpretation and other analysis capabilities for the clinical market, according to CEO Alindrina Mangubat.

Spiral Genetics has to date focused on the academic research market. It offers a suite of standard bioinformatics analysis tools that can run on the cloud or be installed on in-house clusters.

Mangubat told BioInform that in addition to expanding its reach into the clinical genomics market, the company intends to pursue partnerships that will allow it to offer analysis tools for customers in the pharmaceutical industry and the agri-genomics market.

She explained that forming partnerships allows Spiral to focus on its "core competency" — developing upstream bioinformatics tools for things like sequence alignment and variant calling — and at the same time meet customers' requests for genomic data analysis tools that are tailored to their particular needs.

Spiral's platform, Mangubat explained, handles the early stages of genomic data analysis, where "everybody has to do the exact same thing," including alignment, consensus calling, and variant detection. After that, methods for variant filtering and annotation for rare diseases "are very, very different from what you want to use for agri-genomics," which has its own unique challenges, she said.

So, instead of trying to develop bespoke analysis tools for different markets, "we are very focused on the part were our strengths are and we are letting other people whose specialties are in these specialized fields take it from there," she said.

She said that Spiral has some undisclosed customers who are involved in early-stage clinical diagnostic development and agri-genomics and it has begun exploring opportunities in pharma where companies are just now starting to use sequencing to develop better drugs.

She also said that Spiral intends to pursue additional partnerships that will increase its clinical footprint but she declined to disclose who those partners will be.

The agreement between Spiral and Omicia allows the companies to combine their respective products and offer informatics infrastructure that will provide capabilities for analyzing raw sequence data through to identifying clinically relevant genomic variants.

Spiral markets cloud- and cluster-based software for sequence alignment, consensus calling, and variant calling, filtering, and annotation. The platform can be used for analyzing data from targeted, exome, and whole-genome sequencing projects. It claims that its platform can analyze a whole human genome from raw sequence data to a fully annotated list of genetic variants in about three hours.

Users can purchase access to the company's cloud system under a pay-as-you-go model using a credits system that starts at $75 for 50 credits, which can analyze five gigabases of data, and goes up to $2,300 for 2000 credits, which can analyze 200 gigabases of data. Alternatively, they can sign up for an annual subscription that starts at $450 for 500 credits per month to analyze 50 gigabases of data and goes up to $3,500 for 5000 credits per month to analyze 500 gigabases. Customers that need to analyze higher volumes of data can contact the company for special pricing options.

Omicia, meantime, markets Opal, a software-as-a-service variant analysis solution for analyzing and prioritizing disease-causing variants. Its pipeline includes the Variant Annotation, Analysis, and Selection tool, or VAAST, a tool that the company developed for functional interpretation of whole-genome sequence data that helps users identify candidate disease genes and causal alleles (BI 7/1/2011).

Through an app store, Opal offers specific workflows for clinical researchers and CLIA labs to analyze disease mutations in individuals, families, and cohorts. Customers can either use a free version of the tool, which comes with limited functionality such as unlimited storage and an annotation pipeline, or they can purchase a more comprehensive "pro" version that includes access to VAAST, a tool for family tree-based analysis, and features for comparing multiple genomes and sharing analysis results.

The companies aren't disclosing the financial details of their partnership or discussing the marketing strategy for their combined offering.

In a statement, Martin Reese, Omicia's co-founder, president, and chief scientific officer, said that the partnership with Spiral will allow "faster and more accurate interpretation of human genomes for clinical relevance" and "move us closer to a seamless solution from raw sequence data to clinically relevant genomic variants." He declined to provide further comment.

Series A Financing

Spiral's $3 financing, also disclosed this week, was from the venture capital firm Draper Fisher Jurvetson.

Spiral will use the funds to expand its bioinformatics engineering team, explore new marketing campaigns to improve sales, and develop new features for its platform as well as speed up its release cycles, Mangubat told BioInform.

She said the company is looking to double its eight-person headcount. Specifically, the company intends to hire several software developers that have about five years of C++ experience and a bioinformatician with a "heavy" algorithm background. The company is also looking to hire sales and marketing staff.

In terms of its product development plans for the year, Spiral plans to release a proprietary data compression method that will help users shrink large datasets which should make them easier to move around, Mangubat said. The company will also release a tool that will offer improved variant detection capabilities, she said.

She added that the next release of the Spiral Cloud, targeted for later this year, will include an "escort" feature that will make it easier for customers to move their data from Spiral to Omicia's Opal infrastructure for further analysis.

Both Spiral and Omicia are on the list of companies that were tapped by Illumina to develop analysis tools for its BaseSpace applications store last year.

At the time, Mangubat told BioInform that the company was working on integrating its Spiral cloud with BaseSpace so that researchers using BaseSpace would have access to its tools. Meanwhile, Omicia's Reese said that his company planned to integrate its clinical genome interpretation platform with BaseSpace in a manner that would allow users to navigate from Illumina’s cloud to Omicia’s system (BI 8/24/2012).