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Building next-gen castles in the cloud
April 2011
by Jeffrey Bouley  |  Email the author


SEATTLEŚLooking to continue its tradition of offering "high-value, low-cost, 'out-of-the-box' solutions serving the life sciences market," genetic analysis software developer Geospiza Inc. has teamed up with San Carlos, Calif.-based NuGEN Technologies Inc., a provider of sample preparation solutions for clinical samples, to develop a seamless next-generation sequencing (NGS) workflow to accelerate discoveries for large disease research studies.
And, as with so many other things these days, they're going to the cloud with it.
"Geospiza's lab and analysis software tools are focused on making research easier, faster and more cost effective," says Rob Arnold, Geospiza's president. "Combining our GeneSifter preconfigured lab and analysis cloud software with NuGEN's Ovation and Encore reagents enables researchers to follow and document a step-by-step best practice for sample preparation, combined with fully integrated data analysis and other sample information, in one system."
He says Geospiza officially approached NuGEN toward the second half of last year because the cloud-based integration concept was something Geospiza had been mulling over for some time.
"NuGEN has been a customer of Geospiza's for a while now," notes Dr. Yan Zhang, vice president of marketing at NuGEN. "During development of our sample preparation reagents for next-gen sequencing, our scientists found Geospiza's data management and analysis pipeline very easy to use. In addition, we started thinking about incorporating unique features in our reagents, such as controls and indexing adaptors, and thought an integrated solution on the back end that would automatically highlight these sample prep design features will really make life much easier for our mutual customers and expedite their process. From there, the two companies maintained dialogue and began to discuss ways that we could work together to simplify the entire workflow for next-generation sequencing analysis."
Zhang says both companies are very customer-focused and have a strong desire to "fully understand our customers' challenges and come up with strategies to help solve their problems." NuGEN will continue to develop sample preparation solutions while working with Geospiza to provide the most optimal, simplified and integrated laboratory information management and analysis systems for its customers' NGS workflows, Zhang adds, noting: "We hope that the simplified solutions will help accelerate the adoption of genomic analysis for clinical samples and ultimately benefit patient care and advance life sciences."
Arnold says much of the technology is already old hat for both companies, so the question of whether it works isn't the issue. At this point, it's more about ironing out the wrinkles so that users can get the best possible experience, with researchers seeing what they need to from their perspective when they access applications in the cloud, and the lab analysis people getting their own customized view so they can do their part of the work.
Currently, the companies are working with a few early-access customers and getting feedback on the functionality. The next step will be to broaden access to more early adopters this year and get even more feedback before going for any kind of full-fledged commercialization efforts.
"We know the individual technology works," Arnold says, "but we just want to make it as user-friendly as possible."
"Our innovative sample preparation capabilities complement nicely with Geospiza's platform," says Elizabeth Hutt, CEO of NuGEN. "Together, NuGEN and Geospiza are developing a scalable integrated workflow that accelerates throughput and removes sample preparation and analysis bottlenecks in next-gen sequencing."
According to Arnold, the next stage for Geospiza's business is to branch out from a customer base that is largely academic and government research and gain more traction in corporate and other applications.
"We're seeing the NGS technologies moving out of academia and into more direct work in building new drugs, vaccines and diagnostic tools," he notes. "We see substantial opportunities for us in that regard for the next few years. As these next-gen technologies become more routine, the novelty won't be about the technology anymore but about how to get actionable knowledge and democratize the technology so that more people can use it."

Geospiza wins $1.2M grant to add new DNA variant application to GeneSifter software
SEATTLEŚGeospiza Inc. also recently announced that the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) has awarded the company a Phase II SBIR grant to collaborate with researchers at the Mayo Clinic and Weill Cornell Medical College to develop a new application that quickly identifies and visualizes DNA sequence variations found when comparing normal and cancer tissues using Geospiza's GeneSifter cloud computing platform.
"Through this funding, we will be able to attack the biggest challenges researchers face when attempting to develop cancer tests," explains Todd Smith, Geospiza's chief technology officer. "There are substantial DNA variations between normal and cancer tissue. Researchers wanting to develop a new cancer test need to figure out those differences and put them in a biological context. This process requires easy-to-use visual presentation of millions of data points to see those differences. GeneSifter is the ideal platform to deliver this exciting new application."
"The new sequencing technologies are letting us probe cancer biology in ways we've never contemplated before," adds David Smith, professor at the Mayo Clinic. "It's clear that the next generation of diagnostic tests can only be made by effectively combining whole-transcriptome analysis with genome sequences on a per-patient, per-sample basis. The numbers of combinations are daunting. The application developed through this work will be well-suited for translating research observations to actionable clinical tests."
Code: E041112



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