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Geospiza links with SAIC-Frederick
October 2010
by David Hutton  |  Email the author
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SEATTLE—In an effort to potentially accelerate cancer research, Geospiza and Maryland-based SAIC-Frederick Inc. are collaborating to adapt Geospiza's software platform to a new generation of rapid, high-resolution gene sequencing technology.
SAIC-Frederick is an early adopter of cutting-edge, third-generation sequencing technology designed to provide faster, high-resolution DNA sequences for use in cancer research.

The newest second-generation gene sequencers can rapidly produce huge amounts of genetic data, in some cases approaching 3 billion sequences —the equivalent of an entire human genome—in just two days. This advance holds great promise for advancing scientists' understanding of the genetic basis of cancer. It also presents new challenges, especially in regard to managing unprecedented volumes of data and accurately correlating them with patient information.

Geospiza and SAIC-Frederick are collaborating to address these challenges by integrating Geospiza's GeneSifter Lab Edition product for data acquisition and analysis with a third-generation sequencer, PacBio RS, Pacific Biosciences' Single Molecule Real Time (SMRT) biological detection platform.

Having in place a rapid, third-generation sequencing system is expected to accelerate studies into the genetic basis of cancer and to pave the way for more effective treatments. SAIC-Frederick, a contractor for the National Cancer Institute's laboratories in Frederick, Md., is facilitating the collaboration as part of NCI's Advanced Technology Partnerships Initiative, which seeks to reduce the time and cost of developing new cancer treatments.

"Cancer biology is a sweet spot application for next-generation sequencing and systems like the PacBio RS," says Todd Smith, Geospiza's chief technology officer. "SAIC is one of several of our customer sites that are in PacBio's early access partner program, so the work here will extend to other sites."

SAIC-Frederick will use GeneSifter interfaces already in place in its labs to create custom workflows and data analysis unique to SMRT sequencing. SAIC-Frederick will also provide enhancements for systems analysis and for automation. The result will provide researchers with a productive data management system tailored to their needs.
While financial terms of the agreement are not being released, Smith notes that both groups are contributing subject matter expertise to the project.

"SAIC will help us understand the practical issues related to implementing the PacBio system," he says. "With any new system, there is a gap between what we think we can do with the system and what it can really do. We will work with SAIC to incorporate this knowledge to configure workflows within the system."

Geospiza will provide product experience and insights to help SAIC get up and running quickly with the PacBio system.  

"We bring close to 13 years commercial LIMS development to the project," Smith points out. "Additionally, as one of PacBio's early software partners we will be able to leverage this relationship to get information about sample organization and data flow. Some of these insights will contribute to new features in the next releases. In most cases this a learning process that is needed to understand how to best configure existing software components. "

SAIC-Frederick Inc., a wholly owned subsidiary of Science Applications International
Corp.
, is the operations and technical support contractor for the National Cancer Institute's research and development center in Frederick, Md. The latest effort isn't the first time the two companies have worked together.

"SAIC has been a customer for some time," Smith says. "We worked with the group in the early days of Sanger and other labs within the organization using our system to manage their Illumina and 454 labs."

In addition to having a happy customer, Smith notes that success will be measured on whether the work translates to software-enabled workflows that show other groups how to set up their laboratories to support the PacBio system.
 
"In our many sales and customer interactions, we find that labs need a lot of help simply to get started at the bench," he says. "When we load a predefined workflow into the system that has been validated by another lab, or the instrument vendor, folks can see right away what they need to do at that bench and how the technology they've acquired really works."


 
 
Code: E101010

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