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Confirmant Debuts Protein-Centric Database, Says its Biz Model Is Viable


Despite the absence of many regular bioinformatics exhibitors, attendees of the Cambridge Healthtech Genome Tri-Conference in Santa Clara, Calif., last week might have experienced a brief sense of deja vu.… Subscribers: click headline for more

Despite the absence of many regular bioinformatics exhibitors, attendees of the Cambridge Healthtech Genome Tri-Conference in Santa Clara, Calif., last week might have experienced a brief sense of deja vu.

Confirmant, the joint venture between Oxford GlycoSciences and Marconi that was created last summer to build and commercialize a proteomic database [BioInform 6-25-01], debuted the prototype of its first product there with all the fanfare of a 1990s bioinformatics company launch — there were goody bags containing logo-branded calculators, stopwatches, and slick media kits; customer workshops and media briefings; and carefully timed business stories in the New York Times and Wired.

At a time when many in the industry are rethinking the genomic database business model, it seems surprising that a new database vendor would emerge. But Confirmant says its strategy won’t take it down the same path as data vendors before it. Its mission: “To be the leading provider of bioinformation, offering customers a protein-centric view of the genome and a deeper understanding of disease.”

Company officials told BioInform that their so-called Protein Atlas, which will eventually contain experimentally validated data for every protein expressed in as many different tissues as possible, is commercially viable because its content simply won’t be eroded by public-sector efforts.

They said that an approach such as theirs — one that systematically derives proteins from tissue samples and then maps them back to exons on the Golden Path version of the human genome using peptide sequence tags, or PSTs — would be too complex, costly, and massive an undertaking for any public-sector effort.

“High-throughput expertise is required for this and we’re four years ahead of any others who would jump in,” said CTO Jonathan Sheldon.


Global Samples, Co-localized Fragments


Sheldon, a former Roche bioinformatics director, said the Protein Atlas, which currently contains data for proteins encoded by 7,000 genes and is slated to contain data for 10,000 by its launch in June, will be available in XML format “and other options for easy integration into existing infrastructure.” The database will also incorporate the Ensembl database as a reference.

Although early plans indicated that joint-venture partner Marconi, a telecommunications company, would provide IT hosting and broadband services for Confirmant’s customers, Sheldon said, “the feedback at the moment is that people want to integrate the data themselves and take it into their own existing infrastructures, so we’ll do what people want.”

Ultimately Sheldon expects the database to include data for all human genes. It will also be expanded over time, he said, with information on genes linked to time progression of disease states and perhaps eventually protein-protein interaction data.

Confirmant plans to sell royalty-free three-year subscriptions to pharmaceutical and large biotech companies. Sheldon wouldn’t comment on pricing but did not dispute previous reports that annual subscriptions would be priced at £2 million, or roughly $2.9 million.


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