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Ten of the world's leading pharmaceutical companies, together with Britain's Wellcome Trust, are due to confirm today (15 April) that they will fund a US$45-million map of the variations in the human genetic code that could be linked to common diseases.

The map will not be patented and will be given free to the world's research community. It will be made available to researchers as it is being constructed, and is expected to be completed within two years.

The project aims to identify up to 300,000 variations in the 3 billion nucleotide base pairs that make up the human genome. These variations are called single-nucleotide polymorphisms, or SNPs; one SNP is estimated to occur roughly every 1,000 bases.

In the long term it is hoped that the map will lead to more effective medication, such as ‘personalized’ drugs, and to the development of smaller and cheaper drug trials.

In the short term, however, an SNP map is expected to help to reduce the incidence of side effects from existing medicines, and to make the search for genes associated with diseases much faster and cheaper.

For example, by comparing SNP maps of individuals suffering from a disorder such as coronary heart disease with maps of healthy people, researchers hope to identify regions of the human genome where genes associated with the disease might be found.

The Wellcome Trust will contribute $30 million to the project, and has already funded three pilot studies. The SNP Consortium of pharmaceutical companies will contribute the remaining $15 million.

The consortium consists of AstraZeneca, Bayer, Bristol-Myers Squibb, Hoffmann-La Roche, Glaxo Wellcome, Hoechst Marion Roussel, Novartis, Pfizer, Searle and SmithKline Beecham. The identification and analysis of SNPs will be done at centres involved in the international Human Genome Project.

The US National Institutes of Health has already given $30 million in grants over three years for ad hoc SNP-related projects. The idea that pharmaceutical companies could fund a more comprehensive map emerged from discussions two years ago at the US National Human Genome Research Institute, says Alan Williamson, formerly vice-president for basic research at Merck and a member of the institute's governing council.

Williamson says that pharmaceutical companies were initially approached with the idea of forming a profit-making consortium, which would charge for the use of the map. But those companies that agreed to the idea surprised most observers by insisting that the data should be made available free. The Wellcome Trust's involvement was also conditional on full and free access to the data.

Bentley: maps are ‘pre-competitive research’. Credit: WELLCOME TRUST

David Bentley, of the Wellcome Trust's Sanger Centre for gene sequencing, says consortium members regard the project as ‘pre-competitive research’, and have agreed not to see any SNP data before they become public.

But the consortium's members will receive an additional benefit. By helping to ensure that SNP data are freely available, the larger pharmaceutical companies will not be restricted to the many proprietary SNP databases already being developed by smaller genomics companies. Indeed, these companies are absent from the SNP Consortium, which is made up exclusively of established pharmaceutical companies.

Celera Genomics near Washington DC is compiling a proprietary SNP database in parallel with its efforts to sequence the human genome. Its president, J. Craig Venter, says he welcomes the new SNP consortium.

Venter says he considers it to be more of a “public education programme” in SNPs than a threat to companies such as Celera. He adds that he expects considerable demand for Celera's product, which, he says, is the subject of a possible patent application.

Two pharmaceutical companies outside the consortium — Amgen and Pharmacia UpJohn — have already signed up, says Venter, adding that Celera expects to obtain between 20 and 30 million SNPs within the next 18 months, two orders of magnitude more than the SNP Consortium. Celera's database, he envisages, could also be augmented by data from the SNP Consortium.

But Allen Roses, a vice-president of Glaxo Wellcome and worldwide director of genetics, says 200,000 SNPs are enough for most practical purposes, such as clinical trials.

Roses claims that it is too late to patent an SNP map, as the concept is no longer novel. He says that the basic idea has already been patented by Glaxo Wellcome (see above) following a mapping exercise to find genes associated with Alzheimer's disease.

Furthermore, says Roses, companies marketing SNP databases will not be allowed to sell data obtained from the SNP Consortium back to a consortium member.