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Bioinformatics Briefs: Feb 27, 2009


Oxford Gene Tech, Optra Systems, Co-Develop Software

Oxford Gene Technology of Oxford, UK, which provides microarray-based technologies, is partnering with Pune, India based life-sci consultancy Optra Systems, to develop visualization and analysis software.

The collaboration is about visualizing and analyzing data from high- resolution scanners and is now in the testing phase following initial software development, OGT said in a release.

This project is part of the OGT's thrust to help researchers study gene expression in single cells, John Anson, OGT’s R&D Director said in a statement. “Image analysis is an integral part of these developments, and we chose Optra Systems for its expertise and excellent service," he said.

Financial details were not made public.

Genedata Expands Discovery Collaboration with Syngenta

Genedata and Syngenta are collaborating in biomarker discovery on LC-MS and GC-MS metabolomic raw data processing and analysis, according to an announcement.

Syngenta has been using the Genedata Expressionist Refiner Array and Analyst modules to process and analyze microarray data since 2005 and has now added Refiner MS to integrate MS data in biomarker discovery projects.

Syngenta’s decision to use the Genedata Expressionist system for metabolomics research is based on the ability of Refiner MS "to capture very large data sets directly from a wide range of instruments quickly and efficiently, and to visualize and manipulate data from a wide variety of mass spectrometry experiment types such as GC-MS and data dependent LC-MS/MS experiments all in one computer platform," said David Portwood, Head of Metabolomics at Syngenta UK.

"A further major benefit is that we can now integrate all the 'omics' data types in one platform and can perform multivariate stats within the Analyst module avoiding time-consuming exporting and importing of data between software packages and leading, we believe, to greater understanding and insights to the biological processes that are key to the future success of our business,” he said.

Financial terms were not released.

SNP Discovery Company Floragenex Partners with the National Center for Genome Resources

The non-profit research organization National Center for Genome Resources announced it is partnering Floragenex, a privately held genetic technology company based in Eugene, Oregon.

In this collaboration Floragenex will bring its proprietary genomic discovery and application tools to the Illumina sequencing and bioinformatics capabilities of NCGR.

Under the terms of the agreement for which no financial details were released, Floragenex and NCGR will collaborate on services projects for customers focused on the discovery of new markers in crops.

Given the costs and capabilities of DNA sequencing "a new segment of agricultural companies and academic researchers" can apply genomics tools to breeding and research, Nathan Lillegard, CEO of Floragenex, said in a statement.

"The technology platforms that Floragenex provides expedite the discovery of genetic variants and will enable us, together, to be the first to decode the genomes of economically important crops," Gregory May, NCGR Vice President and Genome Center Director, said in a statement.

"As the first Illumina Genome Analyzer Certified Service Provider in North America, our efforts to build strategic partnerships with groups such as Floragenex allow scientists at NCGR to continue to bring the latest in cutting-edge genome analysis platforms to our collaborations and service customers," said May.

GenoLogics Completes Additional Financing

GenoLogics announced it has completed $5 million in financing, which will be applied toward ongoing expansion plans.

The funds will be used to accelerate development and global deployment of an "end-to-end informatics solution for organizations pursuing translational research initiatives," the company said.

The latest round of financing was led by OVP Venture Partners of Seattle, with support from Growth Works and Yaletown Venture Partners of Vancouver.

"We feel positive that the growth GenoLogics has experienced will continue as they expand their footprint in the life sciences software market," Chad Waite, Managing Director at OVP Venture Partners, said in a statement.

"The additional funding will allow us to accelerate deployment of our biomedical informatics product suite, as well as expand our sales and support infrastructure to sustain the rapid increase we are seeing in customer adoption," Michael Ball, CEO of GenoLogics, said in a statement.

Genstruct and Gene Logic Collaborate on Systems Toxicology

In a systems toxicology collaboration, Genstruct of Cambridge, Mass., has signed a partnership agreement with Gene Logic of Gaithersburg, Md..

According to the announcement, Gene Logic will provide its toxicology databases and data on specific compounds obtained by the company's gene expression technology for preclinical and clinical research to clients from the pharmaceutical, biotechnology, consumer products, and related industries.

Using its methodology and expertise in toxicity mechanisms, Genstruct will apply its Causal Network Modeling platform for systems biology to create network models that capture the toxicity potential of any compound.

In Genstruct's work with pharmaceutical clients, it has characterized "complex and poorly understood mechanisms" of toxicity, such as idiosyncratic drug-induced liver injury and hemangiosarcoma, Keith Elliston, president and CEO at Genstruct, said in a statement. Elliston was previously CSO of Gene Logic.

Putting the skill sets of the two companies together stands the chance of revealing a new compound's potential to elicit these types of reactions in man based on animal study data from animal studies, he said.

This strategic partnership will be pivotal in providing integrated solutions spanning across different stages of the discovery value chain to our valuable customers." Anuradha Acharya, CEO, Gene Logic said in a statement.

Genstruct and Gene Logic announced they will run co-marketing initiatives to extend each other's offerings to current and potential clients.

In addition, the companies intend to collaborate in other areas, including personalized or individualized oncology therapy. "Here, Genstruct will engage with Gene Logic to generate gene expression data from patient tumors which will be analyzed using our systems biology platform to arrive at a comprehensive network-level understanding of an individual patient's disease," Ellison said.

Arizona Biomedical Research Commission and 5AM Solutions to Develop Virtual Tissue Bank

The Arizona Biomedical Research Commission and software developer 5AM Solutions announced in a statement they will be developing a centralized, web-based biological specimen tracking software system.

This virtual tissue bank, will provide a consolidated view of tissue samples stored in repositories in a number of Arizona hospitals and research facilities.

Brent Gendleman, CEO and President of 5AM Solutions, said in a statement the company will customize, extend, and host caTissue Suite, which is a biorepository management system developed in the context of the cancer Biomedical Informatics Grid. "The caTissue Suite that we are customizing for the ABRC will help speed the pace of research and foster increased collaboration across a number of institutions," Gendleman said in a statement. 5AM Solutions is a licensed caBIG support service provider.

In an email to BioInform he said his company will be running a hosted, centralized system, which "will receive data feeds from proprietary and home grown systems, in addition to having some institutions use the web exclusively."

The environments with which integration is sought have not yet been determined, he said.

"We are using the caBIG Model Open Source license for our distribution of the software, he said, which means the firm is not charging for that license, only the services, customizations, training, and ongoing support and maintenance and production hardware being executed.

"The software components we are employing are JBoss and MySQL, though Oracle is also an option for others," he said. There is a one-year contract with 2 option years.

Currently, the plan is not to store the omic data that may be produced by the studies conducted by external researchers, he said. But since his firm is also the developer of caArray, the NCI's array management system, he has "a vision for integration across the suite [to include] clinical, tissue, array and imaging data."

"An important factor that led us to partner with 5AM Solutions and adopt caTissue as the platform is our state's Native American population," said Dawn Schroeder, Executive Director of the ABRC. "Of the 22 Native American tribes in Arizona, many have religious beliefs that require any tissue samples they donate be tracked in such a way so that should the donor die, that tissue can be returned to the tribe."

"By customizing the caTissue platform, we will know where these samples are, how much was used, what is left, and what can be returned to the tribe," Dr. Schroeder continued. "The ability to do this is critical to enabling Native American participation in clinical studies as either a donor of tissue or as a human subject."

The ABRC is charged with establishing research programs, evaluating research proposals, and awarding funds. It has approximately $11 million invested in research contracts and currently manages 74 research contracts.

The Scan

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.

Breast Cancer Risk Gene Candidates Found by Multi-Ancestry Low-Frequency Variant Analysis

Researchers narrowed in on new and known risk gene candidates with variant profiles for almost 83,500 individuals with breast cancer and 59,199 unaffected controls in Genome Medicine.

Health-Related Quality of Life Gets Boost After Microbiome-Based Treatment for Recurrent C. Diff

A secondary analysis of Phase 3 clinical trial data in JAMA Network Open suggests an investigational oral microbiome-based drug may lead to enhanced quality of life measures.

Study Follows Consequences of Early Confirmatory Trials for Accelerated Approval Indications

Time to traditional approval or withdrawal was shorter when confirmatory trials started prior to accelerated approval, though overall regulatory outcomes remained similar, a JAMA study finds.