More than two years after it was conceived, and 14 months after it was formally launched, the International HapMap Project has finally told researchers how they can view its data.
Organizers of the project have promised that “some” of the HapMap data will be “released quickly” and with “no conditions,” while other data “can be accessed quickly” by researchers who agree to certain restrictions.
The project said it “is committed to rapid and complete data release, and to ensuring that project data remain freely available in the public domain at no cost to users,” participants wrote in the Dec. 18/25 issue of Nature. The article also reiterated the rationale behind the HapMap Project.
To obtain certain genotype data from the HapMap Project website, users will be required to affirm they will “not take any action (including patenting) that would restrict the access of others to the data within it or share the data with anyone who has not read these terms and conditions and agreed to them.”
Specifically, information in the database about SNPs, SNP assays, and allele and genotype frequencies may be freely downloaded, according to the project’s website. However, users will be required to complete a click-wrap license agreement when they want to view data about the genotypes related to those SNPs. These data will be “gradually released,” according to project organizers. “Once there is a sufficient density of genotype information in a chromosome region to derive haplotype information, the derived haplotypes and the underlying individual genotypes in that region will also be publicly released to dbSNP without restriction,” the project organizers said.
David Altshuler, of the Whitehead Institute for Biomedical Research, and a leader in the HapMap Project, said the main rationale behind the data-release policy was to prevent individuals from using the data to flesh out — and patent — their own gene or mutation maps. “That was something that the funders and the participants felt that, if this public effort was to go forward with the goal of making the information freely available, it would be an unfortunate consequence if someone else scooped up the data and patented it, and then tried to restrict use by the public, who are meant to be the beneficiaries,” Altshuler told SNPtech Reporter this week.
“The intention of this policy is just to say, ‘If you want to use the data, go ahead and do anything you want with it as long as you don’t restrict any one else’s use of it,” he said. When “a sufficient amount of the data” have been deposited into the public domain, which organizers said will likely happen at the end of 2005, “it will be very unlikely that it would be patentable.” [Read more about the rationale behind the policy here.]
“This licensing approach is not intended to block the ability of users to file for intellectual property protection on specific haplotypes for which they have identified associated phenotypes, such as disease susceptibility, drug responsiveness, or other biological utility, as long as public access to, and use of, the data produced by the HapMap Project is preserved,” the project stressed on its site.
According to the Nature article, the consortium believes that SNP, genotype, and haplotype data “in the absence of specific utility do not constitute appropriately patentable inventions.” The group defines “specific utility” as an “association of a SNP or haplotype with a medically important phenotype,” such as disease risk or drug response.
“The [HapMap] project does not include any phenotype association studies,” the authors wrote. “However, the data-release policy does not block users from filing for appropriate intellectual property on such associations, as long as any ensuing patent is not used to prevent others’ access to the HapMap [Project] data.”
Where Does It Stand Now?
The goal of the HapMap Project is “to develop a research tool that will help investigators ... discover the genetic factors that contribute to susceptibility to disease, to protection against illness and to drug response,” the organizers wrote in the Nature paper. The project will study some 270 samples from the United States, Japan, China, and portions of Nigeria, according to Lisa Brooks, program director of genetic variation and genome information for the National Human Genome Research Institute.
Christopher Austin, who advises NHGRI director Francis Collins on issues relateing to translational research, said the HapMap project, which will cost more than $100 million over three years, will haplotype between 80 percent and 90 percent of the human genome. To date, the project has identified 4.8 million SNPs, and expects 6 million by January 2004.
Austin mentioned this status during a pharmacogenomics conference in Washington, DC, last month. He said that “all data will be publicly accessible,” and that a “unique [intellectual property] strategy is being developed to guarantee this.”
A first-pass draft of the HapMap will be developed with 600,000 SNPs spaced at 5kb intervals, and will eventually contain 1 million genotyped SNPs, according to Brooks, who discussed the status of the HapMap Project at the SNP and genome-analysis conference in Chantilly, Va., last month.
On Tuesday, the HapMap Project has released for download 173,974 genotypes, frequencies, and assays for SNPs, and said that the GBrowse viewer “is being updated,” according to its website. In November, the project released more than 13 million genotypes from 145,554 SNPs, as well as “associated frequency and assay data.”
This followed more than 12 million genotypes from 137,964 SNPs submitted in October, and more than 11 million genotypes submitted in September. One month earlier, researchers submitted more than 10 million genotypes and 117,000 SNPs.
“For the full potential of the HapMap to be realized, several things must occur,” the researchers wrote in their Nature article. “The technology for genotyping must become more cost efficient, and the analysis methods must be improved. Pilot studies with other populations must be completed to confirm that the HapMap is generally applicable, with consideration given to expanding the HapMap if needed so that all major world populations can derive the greatest benefit.”