November 1, 2006 (Vol. 26, No. 19)

Proteomic and Genomic Platforms Narrow the Biomarker Search

Pharmaceutical and biotechnology companies generate enormous amounts of complex scientific data from proteomics, genomics, and metabolomics research, which they hope to mine for new drug targets. The management and integration of such data can be accelerated with solutions created by GenoLogics Life Sciences Software ( “We’refocused on providing software for laboratory data and workflow management that allows companies to look at everything in a systems biology context,” says Michael Ball, CEO. The company aims at becoming a leading provider of laboratory and data management software for life science researchers in the drug discovery field.

Although the top pharmaceutical companies spend billions of dollars on proteomics and genomics research, “meaningful results are limited, and you don’t see a lot of new drug targets,” Ball points out. Despite many good data-analysis packages, the experimental data is not being evaluated in terms of their biological context. “If you don’t have biological context and properly managed data, then analysis doesn’t matter much,” he adds.

Proteomics and Genomics Platforms

GenoLogics launched its first product, Proteus, in 2003 to help proteomic researchers narrow the search for biomarkers associated with diseases. Proteus can be installed and operated within a week, compared to months of customization typically needed for other laboratory information products. The open, configurable, and integrating platform manages data from laboratory instruments, software, and analysis tools. Bioinformatics experts can access and extract data and integrate it into other commercial or open-source software. Laboratory workers can configure Proteus to work specifically for them, for instance, to connect activities across several scientific disciplines in a high-throughput environment.

Overall, Proteus transforms the data management process into an efficient and collaborative system to speed biomarker discovery. The platform manages samples to preserve proteins; supports protein arrays and mass spectrometry (MS) through specialized modules; incorporates bioinformatic tools, such as pattern-recognition algorithms; mines, analyzes, and integrates data into leading protein search engines; links disease progression to proteomic profiles to find significant drug targets; and coordinates data across various projects and laboratories.

The same open, configurable, and integrating platform that drives Proteus is also behind Geneus™, a new platform designed for genomics researchers. These researchers at large pharmaceutical firms or academic institutions perform different workflows, including genotyping and gene-expression analysis. Each requires different instrumentation, workflow, and software. “As the field evolves, people want one solution to manage it all,” says Jason Wilson, genomics product manager at GenoLogics.

Even laboratories running the same product, such as commercial microarrays, follow different workflows. With Geneus, researchers can configure and finely tune the process to fit their workflow to maximize efficiency and control costs. Specific modules can be integrated with laboratory instruments and assigned to different personnel for better task management. Geneus also has a quality-control module that captures and processes raw data to quickly flag samples as pass or fail.

Geneus also tracks samples and provides a history of all processes performed on a sample. A LabLink feature serves as an interface for electronic sample submission from collaborators. Users can receive published reports with a powerful reporting engine that allows them to select custom fields.

A few early-access customers will receive the first version of Geneus by the end of 2006, and a general release is planned for early 2007. Four companies have committed themselves to buying Geneus because of past positive experiences with Proteus.

The prominent features of both Proteus and Geneus are configurability and flexibility. “It sounds basic,” says Ball, “but in the high-throughput life science market, it’s hard to build software to handle variability.”

In general, laboratory data management software has a checkered past because it tried to be all things to all people. “We recognize that we cannot be all things to all people and draw on partners to build a more complete solution than we can build by ourselves,” says Ball.

GenoLogics proactively recruits strategic partners to enhance Proteus and Geneus and add value for their customers. For instance, the company is working to make Geneus compatible with Affymetrix’ GeneChip® technology, as well as other gene-analysis products that will be released in the near future.

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