Getting it right the first time

Sirius Genomics and Golden Helix collaborate on sepsis diagnostic development

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BOZEMAN, Mont.—Vancouver-based Sirius Genomics, a developer of companion diagnostics, and Golden Helix—dubbed "the best in the world at data crunching" by Sirius CEO Chris Wagner—will work together to develop a diagnostic to identify individuals who respond favorably to vasopressin and similar compounds used in the treatment of septic shock and related conditions.

Unlike other situations where the selection of drug therapy can rely on trial and error without endangering the patient, with septic shock, "you have to get it right the first time," Wagner notes. Under the agreement, Golden Helix will apply its expertise and technologies in SNP and copy number variant analysis and predictive modeling to advance development of Sirius' diagnostic pipeline.

Septic shock occurs when sepsis (a severe infection spread via the bloodstream, characterized by a whole-body inflammatory state) leads to life-threatening low blood pressure. In the United States, sepsis is the second-leading cause of death in non-coronary ICU patients, and the 10th most common cause of death overall according to data from the CDC, notes Andy Ferrin, Golden Helix's executive vice president of business development. Sepsis occurs in 1 to 2 percent of all hospitalizations, and accounts for as much as 25 percent of intensive care bed utilization with mortality rates that range from 20 percent for sepsis to more than 50 percent for septic shock. The number of sepsis cases per year has been on the rise in the United States and is expected to reach one million cases per year.

Golden Helix specializes in SNP and copy number analysis, genetic association software and analytic services.

"Our technologies empower scientists to determine the genetic causes of disease, develop genetic diagnostics, and advance the quest for personalized medicine," Ferrin states.

He notes that the company's products are used by hundreds of researchers at the world's top pharmaceutical, biotech and academic research organizations and have been cited in more than 300 peer-reviewed publications.

"For our work with Sirius," he observes, "we use an advanced form of tree-based modeling, known as FIRMplus, which is based on Formal Inference-based Recursive Modeling, or FIRM. At Golden Helix, we believe the key to the amazing potential of genetic discovery is empowering researchers to creatively explore and interact with genetic data. So in everything we do, we challenge the belief that scientists must spend a large portion of their time writing and debugging code, or fighting with difficult tools and data. In fact, we believe this is one of the most limiting constraints on the pace of genetic discovery today, and that we should be enabled by tools, not burdened by them. The way we challenge this status quo is by providing tools and services that inspire the discovery process and accelerate research."

Wagner notes that his company has a very broad interest in developing companion diagnostics that are closely tied to therapeutic decisions—in fact, he says it extends to all the drugs on the market.  

"We focus on drugs that don't work on everyone," he says. "Phase I and Phase II studies are too small in sample size to do genetic studies. Talk to the contrary is nonsense." Instead, he notes, Sirius' work relies on "1,000 computers linked together for two months" to work with thousands of samples and millions of data points.

Golden Helix helps Harvard researchers study disease heritability

BOZEMAN, Mt.—Golden Helix Inc. also recently announced a collaboration with Harvard School of Public Health (HSPH) under which Golden Helix is refactoring Pedigree-Based Association Tool (PBAT,) HSPH's software for studying disease heritability in families.

Originally developed eight years ago by Dr. Christoph Lange of HSPH, PBAT is an extensive array of advanced statistical routines used in the design and analysis of family-based SNP and CNV association studies. A command-line version of the software is available from the university free of charge for academic use, but HSPH has granted Golden Helix an exclusive license to develop and distribute a commercial version of the software. At the onset of this partnership, Golden Helix created a graphical user interface to PBAT as well as extensive documentation, all of which are now incorporated into the company's SNP & Variation Suite (SVS) 7.

Golden Helix has been working with HSPH researchers to fundamentally rewrite the original PBAT code, providing the additional software engineering expertise required to dramatically improve performance on large-scale data and to build a more robust code base that will streamline the implementation of new methods.

"Working 'under the hood,' so to speak, we were able to build a platform that facilitates method improvements, runs faster, is more stable, and eliminates parameter constraints," says Gabe Rudy, Golden Helix's vice president of product development. "Users will now be able to analyze larger family structures on more than one marker at a time, and with more options for interaction variables, thereby increasing the power to detect disease heritability."

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