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Cypher Genomics’ Analytics Tech Gains Some Cred in Illumina Deal

It’s probably just a matter of time before a new company combines the rapidly advancing technologies of genome sequencing, genetic diagnostics, and Big Data to become the Google of bioinformatics.

Cypher Genomics would like to claim that title, though it’s too early to tell if the three-year-old San Diego startup will be able to pull it off.

Today, Cypher says it is joining forces with San Diego-based Illumina (NASDAQ: ILMN) in a deal that lets Illumina’s sales force promote Cypher’s biomarker discovery services while pitching their own technology and services.

It seems like a sweet deal for Cypher, given that Illumina leads the market in next-generation gene sequencing technologies used by big pharma, biotech, government, and academic research institutions. Cypher currently has 10 employees, while Illumina has about 3,000.

“We’re a small, virtual company, so obviously getting access to Illumina’s large sales force is great,” says Adam Simpson, a life sciences executive and lawyer who joined Cypher earlier this year as president and chief operating officer.

Cypher’s agreement with Illumina also provides some credence to “Coral,” the analytic software Cypher has been developing to pick out individual genes in an ocean of DNA material. Cypher says its analytic technology also can be used to determine if a particular genetic variant is harmless or a troublemaker—and if it is a trouble-making gene, to see if it can be correlated with specific diseases and disorders.

Cypher Genomics founding CEO Ashley Van Zeeland

Ashley Van Zeeland

Work on the kind of quantitative analytics and computational tools needed to screen millions of DNA bases, and to identify and classify thousands of genes, began at the Scripps Translational Science Institute (STSI), where director Eric Topol was working with Nick Schork, an expert in bioinformatics and genomic medicine, Ali Torkamani, an expert in drug discovery and experimental medicine, and Ashley Van Zeeland, a neuroscientist working in Schork’s lab.

All four co-founded Cypher Genomics in 2011—and Van Zeeland continues to serve as CEO. She says unnamed angel investors provided most of the necessary startup capital.

Cypher later began working with both STSI and Scripps Health on the “Wellderly Study,” which set out in 2011 to build a database made up of the whole genomes of thousands of elderly people, at least 80 years old, who were free of major diseases. The idea was to create a “reference genome” of healthy people (who presumably had few aberrant genes) that could be used as a basis of comparison. Through its strategic collaboration with STSI, Cypher Genomics gained commercial rights to use the Wellderly database in clinical studies.

Now, through its partnership with Illumina, Cypher is offering its genome analysis platform to pharmaceutical companies and other big customers. By comparing the genomes of patients enrolled in a drug trial against the Wellderly database, Cypher says it can identify genetic disparities in a patient group far more accurately.

In this way, Cypher says its technology can resolve the “signal-to-noise” problem that makes it difficult for researchers to find important biomarkers in small sample sizes of a few hundred patients or less, the size typically selected for early-stage drug development. With the approach that Cypher is taking, identifying key genetic markers becomes more of a pattern-recognition problem—albeit one that requires comparing enormous sets of genomic data, with each set involving billions of DNA base pairs.

So Cypher’s aspirations to become the Google of bioinformatics may not be too far-fetched, after all.

In a statement today, Van Zeeland says, Cypher’s biomarker discover service “has a proven track record of success with pharmaceutical companies to discover the genetic bases of response to drug therapy.”

In addition to identifying the variant genes responsible for disease, Cypher says it can use its computational analytics to identify additional genetic markers that correlate with patients who respond to a particular drug therapy.

Identifying the variant genes responsible for disease, and correlating the genes that correspond with different drug therapies represents the basis of precision medicine. But it is a burgeoning field of R&D, and Cypher Genomics hardly has the field to itself. The list of other startups working to commercialize their own technologies for using genomic data include Knome, SolveBio, Appistry, Silicon Valley Biosystems, Ingenuity, DNAnexus, and Curoverse.

Henry "Hank" Nordhoff

Henry “Hank” Nordhoff

In a separate statement, Cypher said that Gen-Probe founder and CEO Henry “Hank” Nordhoff recently joined the company’s board as executive chairman. The company also named Genentech co-founder Herb Boyer and former FDA commissioner Andrew von Eschenbach as directors.

Simpson emphasized that Nordhoff, Boyer, and von Eschenbach bring deep experience in biomedical diagnostics, biotechnology, and regulatory matters to Cypher’s already-prominent leadership.

“These folks wouldn’t be interested in [Cypher] if they didn’t think there wasn’t a big business to be developed here,” Simpson said.

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  • Hisham ElDai

    This sounds to be an exciting thrust into the field. Big Data is becoming increasingly relevant to bioinformatics. Having integrated sequencing technology with computational approaches will perhaps streamline the process of analysis. However for multi dimensional data we’re yet to see any breakthroughs that present excellent and scalable algorithmic solutions that tackle problems outside the theoretical framework.