Sirius Genomics will work with bioinformatics firm Golden Helix to develop companion diagnostics directed at septic shock and related conditions, the firms said last week.
Vancouver, Canada-based Sirius is using arrays to develop a test to identify individuals who respond to the hormone vasopressin and similar compounds for the treatment of septic shock. The firm recently completed a genome-wide association study to identify potential markers for the test, and will draw on Bozeman, Mont.-based Golden Helix's expertise in SNP and copy number variant analysis and predictive modeling as it moves forward with diagnostic development, according to a company official.
Kamran Alam, senior director of business development at Sirius, told BioArray News last week that the privately held company operates under a "virtual model," outsourcing its bioinformatics needs, and found Golden Helix to be an "ideal partner" for working with GWAS data.
He said that Sirius conducted a GWAS with Illumina's Human1M-Duo DNA Analysis BeadChip as the first step in developing a companion diagnostic for vasopressin. The cohort for the study, which wrapped up in the spring, included " several of hundreds of patients."
While the firm has used arrays for its discovery work, Sirius has not yet settled on a technology platform for its future test. "Given the need for quick turnaround time and other product attributes" — plus the fact that it is "not likely that large a panel of SNP-based biomarkers [will] be taken forward" — an array "may not provide the ideal platform," Alam said.
"We will analyze the various options available to us and choose [a platform] in the near future," Alam added. "The technology space we are in is changing at an amazing pace and offers numerous opportunities for companies such as ours."
Founded in 2001, Sirius is developing a menu of companion and pharmacogenomic tests. According to the company's website, it has worked in the past few years with partners at Vanderbilt University in Nashville, Tenn., and Assistance Publique-Hôpitaux de Paris in France to develop another pharmacogenomic test intended to assess responsiveness to recombinant human activated protein C, sold by Eli Lilly as Xigris, in patients with severe sepsis at high risk of death.
Sepsis is a severe infection spread via the bloodstream, characterized by a whole-body inflammatory state that can lead to life-threatening low blood pressure. According to the US Centers for Disease Control and Prevention, septicemia was the tenth leading cause of death in the US in 2007, the most recent year for which statistics are available.
It is unclear if Sirius is working with the same partners on its more recent study. Alam declined to elaborate, citing confidentiality.
The company raised $6.3 million in Series A financing in 2006, and has signed two contribution agreements with the National Research Council of Canada's Industrial Research Assistance Program to receive an undisclosed amount of funding to support its test development programs, the most recent of which was inked in October.
Bioinformatics Department for Hire
While Golden Helix is known for its genetic association software, such as its recently upgraded SNP & Variation Suite 7 analysis tool, the 12-year-old company also offers analytical services, and has partnered with other companies developing companion and pharmacogenetic diagnostics in the past (BAN 7/27/2010).
Andy Ferrin, executive vice president of business development, told BioArray News last week that the company has done "several" deals similar to the one with Sirius. For instance, Golden Helix has partnered with LineaGen, a Salt Lake City-based diagnostics company, to develop predictive models and tests for autism and multiple sclerosis, he said.
In such arrangements, Golden Helix "typically acts as though we are our client's own bioinformatics department," said Ferrin. "We assist in study design and plating strategies, defining the types of experiments to be run and on what sort of platform," he said.
As an example of how Golden Helix assists in study design, Ferrin noted that for "one potential new client, we are suggesting a two-phased approach that employs whole-exome sequencing on a relatively small number of cases, followed by a validation phase that utilizes custom, highly targeted microarrays to mitigate cost while increasing sample size and, therefore, statistical power."
Once the samples are run for a given project, Golden Helix performs all of the data preparation, quality analysis, analysis, and predictive modeling. It also designs and performs the analytical steps required for biomarker validation, Ferrin said.