Building next-gen castles in the cloud

SEATTLE—Looking to continue its tradition of offering"high-value, low-cost, 'out-of-the-box' solutions serving the life sciencesmarket," genetic analysis software developer Geospiza Inc. has teamed up withSan Carlos, Calif.-based NuGEN Technologies Inc., a provider of samplepreparation solutions for clinical samples, to develop a seamlessnext-generation sequencing (NGS) workflow to accelerate discoveries for largedisease research studies.

And, as with so many other things these days, they're goingto the cloud with it.

"Geospiza's lab and analysis software tools are focused onmaking research easier, faster and more cost effective," says Rob Arnold,Geospiza's president. "Combining our GeneSifter preconfigured lab and analysiscloud software with NuGEN's Ovation and Encore reagents enables researchers tofollow and document a step-by-step best practice for sample preparation,combined with fully integrated data analysis and other sample information, inone system."

He says Geospiza officially approached NuGEN toward thesecond half of last year because the cloud-based integration concept wassomething 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 developmentof our sample preparation reagents for next-gen sequencing, our scientistsfound Geospiza's data management and analysis pipeline very easy to use. Inaddition, we started thinking about incorporating unique features in ourreagents, such as controls and indexing adaptors, and thought an integratedsolution on the back end that would automatically highlight these sample prepdesign features will really make life much easier for our mutual customers andexpedite their process. From there, the two companies maintained dialogue andbegan to discuss ways that we could work together to simplify the entireworkflow for next-generation sequencing analysis."

Zhang says both companies are very customer-focused and havea strong desire to "fully understand our customers' challenges and come up withstrategies to help solve their problems." NuGEN will continue to develop samplepreparation solutions while working with Geospiza to provide the most optimal,simplified and integrated laboratory information management and analysissystems for its customers' NGS workflows, Zhang adds, noting: "We hope that thesimplified solutions will help accelerate the adoption of genomic analysis forclinical samples and ultimately benefit patient care and advance life sciences."

Arnold says much of the technology is already old hat forboth companies, so the question of whether it works isn't the issue. At thispoint, it's more about ironing out the wrinkles so that users can get the bestpossible experience, with researchers seeing what they need to from theirperspective when they access applications in the cloud, and the lab analysispeople getting their own customized view so they can do their part of the work.

Currently, the companies are working with a few early-accesscustomers and getting feedback on the functionality. The next step will be tobroaden access to more early adopters this year and get even more feedbackbefore going for any kind of full-fledged commercialization efforts.

"We know the individual technology works," Arnold says, "butwe just want to make it as user-friendly as possible."

"Our innovative sample preparation capabilities complementnicely with Geospiza's platform," says Elizabeth Hutt, CEO of NuGEN. "Together,NuGEN and Geospiza are developing a scalable integrated workflow thataccelerates throughput and removes sample preparation and analysis bottlenecksin next-gen sequencing."

According to Arnold, the next stage for Geospiza's businessis to branch out from a customer base that is largely academic and governmentresearch and gain more traction in corporate and other applications.

"We're seeing the NGS technologies moving out of academiaand into more direct work in building new drugs, vaccines and diagnostictools," he notes. "We see substantial opportunities for us in that regard forthe next few years. As these next-gen technologies become more routine, thenovelty won't be about the technology anymore but about how to get actionableknowledge and democratize the technology so that more people can use it."

Geospiza wins $1.2M grant to add new DNA variantapplication to GeneSifter software

SEATTLE—Geospiza Inc. also recently announced that theNational Human Genome Research Institute (NHGRI) of the National Institutes ofHealth (NIH) has awarded the company a Phase II SBIR grant to collaborate withresearchers at the Mayo Clinic and Weill Cornell Medical College to develop anew application that quickly identifies and visualizes DNA sequence variationsfound when comparing normal and cancer tissues using Geospiza's GeneSiftercloud computing platform.

"Through this funding, we will be able to attack the biggestchallenges researchers face when attempting to develop cancer tests," explainsTodd Smith, Geospiza's chief technology officer. "There are substantial DNAvariations between normal and cancer tissue. Researchers wanting to develop anew cancer test need to figure out those differences and put them in abiological context. This process requires easy-to-use visual presentation ofmillions of data points to see those differences. GeneSifter is the idealplatform to deliver this exciting new application."

"Thenew sequencing technologies are letting us probe cancer biology in ways we'venever contemplated before," adds David Smith, professor at the Mayo Clinic."It's clear that the next generation of diagnostic tests can only be made byeffectively combining whole-transcriptome analysis with genome sequences on aper-patient, per-sample basis. The numbers of combinations are daunting. Theapplication developed through this work will be well-suited for translatingresearch observations to actionable clinical tests."