By Matthew Willett
Making medicine personal by finding therapeutic drug targets from human genome data is the goal of the multicompany Functional Genomics Consortium.
Genaissance Pharmaceuticals Inc., of New Haven, Conn., last Friday joined the existing members of the consortium, Hyseq Inc., of Sunnyvale, Calif.; Cytoclonal Pharmaceuticals, of Dallas; and GEMA (Grupo de Estudios Multicentros en Argentina).
The inclusion gives Genaissance access to the AtlasBase database, a complete collection of available gene sequences with enhanced functional annotations. All consortium members get access to the AtlasBase database, compiled by consortium member Molecular Simulations Inc., of San Diego, a subsidiary of Pharmacopeia Inc.
Consortium members also receive access to GeneAtlas, a collection of functional annotations that characterize gene products to be selected as targets for drug discovery efforts.
Consortium Director David Edwards, of Molecular Simulations, said the aim of the consortium is targets.
"The goal is to assign protein function to as much of the proteome as possible," Edwards told BioWorld Today. "The way we're doing that is through a computational analysis, a high-throughput pipeline analysis of protein sequences from the genome, and we use a combination of methods to do it: traditional bioinformatics, sequence-based methods, and incorporating some of the 3-D protein analysis techniques [Molecular Simulations] has been developing as a company for about 15 years."
Since its launch in June of last year the consortium has been busy. It has licensed high-throughput annotation technology from Rockefeller University in New York and mapped the V. cholerae genome. That effort took the consortium only seven days.
Farming protein function data can end up yielding a bumper crop of targets.
"We increased the annotation of cholera by 22 percent over what was available in the public sector - that's about 600 new potential targets for cholera," Edwards said. "If we can increase the targets by 20 percent in the human genome, even if you take the 40,000 sequence number that's been announced, you're talking about another 8,000 potential targets above traditional bioinformatics methods."
And companies aren't taking the opportunity the consortium offers lightly. John Ford is the vice president of functional genomics at Hyseq. He said the consortium plays an important role.
"I think it's helping to better annotate the gene sequence for the discovery of therapeutic proteins," Ford said. "As a company working in the biopharmaceutical area, it's very important for us because it's helping us to identify more protein candidates for our research pipeline."
In essence, Edwards said, the consortium is a lifeboat for drug discovery.
"The bottom line is we've been able to demonstrate that we have technology that enables you to identify functions for protein targets that other traditional methods don't," he said. "We're applying both expertise on the protein side and the chemistry side in a high-throughput manner to help people stop drowning in this flood of genomic data." n