By Uduak Grace Thomas

Bioinformatics startup PanGenX is betting that its semantic approach to data integration will ultimately help drug developers and diagnostic firms develop more personalized treatments.

The firm, based in Auburndale, Mass., intends to help pharma and diagnostic customers integrate proprietary and public data in "meaningful ways" and then run analyses that reveal information on individuals' responses to treatment, Jeremy Sohn, PanGenX's chief operating officer, explained to BioInform this week

The company markets the PanGenX Knowledge Base, which uses a linked data approach to aggregate pharmacogenetic data, results from peer-reviewed literature, health outcomes, and claims data. It relies on a set of proprietary ontologies that specify scientific, clinical, and business concepts and relationships to structure that data for querying and analysis.

Among the data included in the knowledgebase is a version of the National Center for Biotechnology Information's Single Nucleotide Polymorphism Database, or dbSNP, that improves on the publicly available resource, according to PanGenX.

The company's version, dubbed LD-SNP, offers a cleaner, normalized version of the public resource, which makes it possible to find additional variants that aren't currently associated with some genes in dbSNP, Sohn explained.

For example, he said, dbSNP's record of the DPYD gene which encodes for the dihydropyrimidine dehydrogenase enzyme that is involved in a metabolic pathway reports about 6,000 variants for the gene, while PanGenX's approach identified nearly 12,000 variants.

This data, combined with the company's semantic-based approach to analysis, makes it possible to map and compare polymorphisms between different individuals as well as calculate distributions of variants from a gene, drug, or disease perspective, PanGenX said.

The product also includes so-called PURL (Persistent Uniform Resource Locator) Nexus, or Plexus, technology, which lets the system combine data from the knowledgebase with remote customer data.

Currently, PanGenX offers two versions of its knowledgebase under a software-as-a-service business model: PanGenx-KB, priced at $250,000 per year for a site license, is geared toward pharma and diagnostic companies; while PanGenX-KB Professional, priced at $35,000 per year, is meant for academic and commercial research groups and labs.

Continue reading here:
PanGenX Takes Semantic-based Approach to Data Integration, Analytics for Personalized Medicine