Far ahead of schedule, and with a large new cash infusion, the International HapMap Consortium may be set to finally change the balance of the pharmacogenomics world.
The information the HapMap Project places in the public trust may render obsolete some proprietary databases, while boosting the availability of drug targets. The consortium said this week that its first draft is expected to be ready by the end of this month — eight months ahead of time.
The project’s $3.3 million in new funding, announced this week, supports an expansion of the map by an additional 4.6 million SNPs — a five-fold increase, according to a HapMap Consortium statement. Mountain View, Calif.-based Perlegen, through a donation of “in kind” services, will test the additional SNPs, increasing the map’s density to one SNP per 600 bases from one per 3,000.
But Perlegen’s expansion of the HapMap’s coverage comes at a price for other players in the genotyping realm — especially those in the private sector. The HapMap’s expanded coverage “devalues Genaissance’s haplotype databases,” Michael Phillips, director of pharmacogenomics for Genome Quebec, said after his presentation at the Molecular Diagnostics meeting this week in Princeton, NJ.
Genome Quebec, a major contributor to the consortium, and others will use the HapMap to help develop new drugs and move new molecular diagnostics into the clinic, he said.
But don’t count out companies like Genaissance just yet. “They still have an edge — they have very detailed maps” in particular areas, Phillips said. “But the longer this goes on, and the better the tools are from other people, the balancing act will shift,” he added.
Genaissance has said in the past that the HapMap project poses no threat to its business. The companymaintains a large database of haplotypes known as HAP Markers, which it seeks to associate with clinically relevant genes Its database contains information on more than 8,000 of these genes, according to Genaissance.
In his role at Genome Quebec, Phillips is in the process of putting together a clinical laboratory to make use of HapMap data, beginning with markers related to ADME/toxicity and cardiovascular risk. Once his lab has validated a set of markers, the data should be able to “tell people who should get what medication, where, how, and what,” said Phillips. “And that can then be miniaturized, but more robustly on a very small platform that can be run in an HIV clinic.”
Of his talk at the Molecular Diagnostics conference, Phillips said, “The point I was really trying to make today is that I think the paradigm of what a diagnostic assay is is changing a little bit — and I think haplotypes are going to be a useful tool, coupled with functional markers.”
It’s difficult to tell whether drug makers are finding the HapMap project useful. Phillips believes that only the project’s completion will tell for sure, but he cites a Nature Genetics research paper by David Goldstein [see Pharmacogenomics Reporter, 2/3/05 for an interview] and colleagues regarding ADME and haplotype tags as a sign of progress in associating therapeutically important phenotypes with the consortium’s information.
Despite the project’s near completion, drug makers have put surprisingly little funding into its final stage. Of the HapMap Consortium’s $3.3 million in new funding, the two main pharmaceutical partners, Bristol-Myers Squibb and Pfizer, contributed $100,000 each, the consortium said. In contrast, the Wellcome Trust of the United Kingdom contributed $624,000, Genome Canada and Genome Quebec contributed $260,000 collectively, Perlegen Sciences contributed “at least” $1.2 million of in kind services, and the US National Human Genome Research Institute contributed $1 million.
The two pharmaceutical companies were original partners of the SNP Consortium, some of whose funding and expertise were donated to the HapMap Consortium in its infancy. Genome Quebec’s Phillips attributes the companies’ contributions to the fundraising prowess of Arthur Holden, chairman and CEO of the SNP Consortium, although he doesn’t see the relative amount of their donations as indicative of lesser interest in the project.
“I think Arthur said, ‘We have a little bit more to do, do you guys think that you could find 100K here or there to help us finish?’” said Phillips.
Bristol-Myers Squibb and Pfizer could not be reached for comment by press time.
The International HapMap Consortium has a total budget of $135 million, and consists of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States. The US portion of the project is led by the NHGRI, which coordinates the contributions of the 19 US National Institutes of Health organizations that contributed funding.
The HapMap Consortium recently ended its computer-based click-wrap license restrictions, making HapMap data completely available to the public as of mid-December. It can be found here.