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Advaita Using SBIR Funds to Develop New Methods for Pathway Analysis

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NEW YORK (GenomeWeb) – Advaita Corporation has received a three-year $1.76 million Phase II Small Business Innovation Research (SBIR) grant from the National Institutes of Health to develop informatics methods for analyzing gene expression data in the context of signaling and metabolic pathways to help researchers better understand disease mechanisms and identify more effective treatments.

Specifically, the grant, which is aministered by the National Institute of General Medical Sciences, will support the company's efforts to develop and implement a method to identify disease subtypes and subgroups of patients with specific disease phenotypes; as well as biological pathway signatures that are linked to specific diseases or are indicators of drug response. The current grant builds on a $150,000 grant that Plymouth, Mich.-based Advaita received from NIGMS last year to demonstrate the feasibility of its approach.

The purpose of the proposed method is to provide researchers with a tool that allows them to compare gene expression data from individual samples at the pathway level, Andrew Olson, Advaita's VP of business development, explained to BioInform. Unlike all current methods, which compare groups of samples with groups of controls — treated versus untreated samples, for instance — "this new method will allow comparisons of any individual sample against a contrast," Olson said.

In the case of cancer, this individualized analysis would offer a more fine-grained look at the characteristics of the tumor in question and researchers would be able to define groups of patients with similar pathway-level profiles. They could then use the tool to identify a "disease fingerprint" or pathway profile that is common to patients within the subgroup and also look for new or existing drugs that would target those specific pathways.

The company is mulling whether to incorporate the method, once it's developed, into its existing software or to offer it as a standalone application, Olson said. Currently the company sells a desktop application called PathwayGuide, which is used to analyze signaling and metabolic pathways from 12 organisms including human, rat, mouse, zebrafish, pig, Arabidopsis, and fruit fly — customers select the organisms whose pathways they want access to when they purchase the solution.

The tool lets users compare data from their experiments to pathways from publicly available resources such as the Kyoto Encyclopedia of Genes and Genomes and Reactome, and it identifies parts of pathways that are up-regulated, down-regulated, or unaffected in given phenotypes based on gene enrichment and perturbation analysis. The platform is patronized globally by biological researchers in academia and industry including Columbia University, New York University School of Medicine, Brown University, and Karmanos Cancer Institute.

First time Pathway-Guide users get a free 30-day trial after which they have to pay an annual subscription for continued access. Advaita didn't disclose exactly how much it charges for-profit organizations and companies but base subscription pricing for academic institutions starts at $1,995 for a single academic user license, which covers analysis on pathways for both KEGG and Reactome for a single organism, Olson said. The price climbs if pathways from additional organisms are added.

Advaita is also preparing to kick off a beta for a web-based version of its software that will be called iPathwayGuide and will offer the same capabilities as the desktop version in addition to a few new ones and will also be more user-friendly than its predecessor, Olson said. The company has already signed up almost 100 people to participate in beta, which should launch in early May. Advaita plans to launch iPathwayGuide at the end of May during the European Society for Human Genetics meeting in Milano, Italy. The company is still mulling pricing.

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