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High-throughput triple team
August 2008
by Amy Swinderman  |  Email the author
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BASEL, Switzerland—As Novartis Pharma AG continues to focus on gene expression research, the Swiss pharma recently teamed up with Applied Biosystems and Integromics SL to develop a platform for seamless analysis of real-time gene expression data produced during biomarker analysis.

The new solution was borne out of a 2007 co-development and marketing agreement between Applied Bio and Integromics that married Integromics' Real-Time StatMiner software with Applied Bio's line of real-time polymerase chain reaction (PCR) systems and TaqMan arrays. Novartis, which recently used TaqMan in a large-scale pilot study, assisted with the collaboration. Financial terms were not released.

Novartis provided the first level of specifications and helped review the various versions of the software. Although the integrated solution was tailored to Novartis' gene expression initiatives, it can also assist other researchers who need to analyze large volumes of real-time gene expression data in their drug discovery research projects without the hassle of dealing with multiple applications and interfaces.

TaqMan is a 384-well micro fluidic card designed for use with Applied Bio's 7900HT Fast Real-Time PCR System to perform hundreds of real-time PCR reactions simultaneously. TaqMan Custom arrays can be designed to a researcher's specifications using any of Applied Bio's 50,000 inventoried TaqMan Gene Expression Assays and nine array formats.

StatMiner provides quantification analysis of gene expression data through a combination of interactive visualization, advanced statistics and data mining tools. Real-Time StatMiner Software, which also enhances quality assurance and quality control, ensures accurate differential expression results from large datasets and multiple endogenous control genes. A stand-alone application, StatMiner is also available as an integrated guide within other leading laboratory data analysis systems.

Novartis, which is leading an initiative to promote the use of gene expression biomarkers in drug development studies, feels the most striking feature of the integration is the ability to analyze raw data as soon as it becomes available, according to Dr. Olivier Grenet, head of the Molecular Biology group at Novartis Investigative Toxicology.
"If there are any outliers in the analysis, they can be easily identified and they no longer interfere with the biological interpretation of data," Grenet says.

Xavier Cristina, Applied Bio's European manager for business development in functional analysis, says the solution is the first product including sophisticated algorithms for real-time PCR data analysis from Bioconductor containers.

"It will help the use of gene expression data by real-time PCR in regulated environments like clinical trials for drug development," Cristina says. "Without such data analysis, data may not be acceptable by FDA if used for drug submission."

Integromics Commercial Director Imad Yassin says working with Novartis on the solution has enriched Integromics' knowledge of researchers' needs for high throughput analysis.

"We believe in building solutions through collaborations," Yassin says. "This solution was driven by the fact that Novartis' clients have always been adamant about the need for high-throughput analysis, and Novartis provided a blueprint of what this solution should look like. The Real-Time StatMiner application is now able to accommodate both large and small-scale projects, while continuing to deliver high quality results in all cases." DDN
 
Code: E080804

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