Mapping of human genetic variation will speed search for disease genes
BETHESDA, Md., Fri., Dec. 10, 2004 – The International HapMap Consortium today announced that it is ending computer-based "click wrap" license restrictions on data generated by its effort to create a map of human genetic variation. As a result, all of the consortium's data are now completely available to the public, a move that will provide researchers with even easier access to tools for identifying genetic contributions to disease.
The consortium is developing a map of common patterns, or haplotypes, of human genetic variation that can be used as a resource for scientists searching for genes related to health and disease. To create the HapMap, DNA was taken from blood samples collected by researchers in China, Japan, Nigeria and the United States. No medical or personal identifying information was obtained from the 270 individuals providing the samples. However, the samples are identified by the population from which they were collected.
The $130 million project, which was launched in October 2002 and is expected to be completed in September 2005, is a public-private partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States. The U.S. component is led by the National Human Genome Research Institute (NHGRI) on behalf of the 19 institutes, centers and offices of the National Institutes of Health (NIH) that contributed funding. For more information on the International HapMap Project, see http://genome.gov/10001688.
From the outset, the consortium followed the example of the Human Genome Project and made most of its data quickly and freely available through public databases on the Internet. However, concerns existed that outside groups might be able to combine some of the HapMap data with their own data to generate patentable inventions – a process referred to by some as "parasitic patenting." Such patents could potentially be used to exclude other researchers from being able to freely use the HapMap data. To prevent this from happening, the HapMap consortium required users to sign, using a simple mouse click from their computers, a free, non-exclusive, non-royalty-bearing licensing agreement to obtain access to certain types of data the project had collected on individuals' DNA sequences, specifically the genotypes. Under terms of that license, users agreed not to prevent others from using the individual genotype data and to share data only with those who had also agreed to this condition.
"The licensing agreement was quite non-restrictive and enabled most researchers to use HapMap data as they wished. However, there was an unavoidable consequence of the license: it did prevent HapMap data from being incorporated into other public genomic databases," said NHGRI Director Francis S. Collins, M.D., Ph.D. "We are pleased that researchers around the globe will now have swift and easy access to all HapMap data, free of any restrictions."
Several recent developments prompted the consortium's decision to drop the licensing requirement. First, consortium researchers already have publicly released data on about one million single nucleotide polymorphisms (SNPs) in the individual DNA samples that have been genotyped for the HapMap project. Second, Perlegen Sciences, Inc., of Mountain View, Calif., has publicly released genotype data on about 1.6 million SNPs. Third, new methods have been developed to analyze the data and are being used to determine the genome-wide patterns of genetic variation in the HapMap data. These advances led the consortium to conclude that the patterns of human genetic variation can readily be determined clearly enough from the primary genotype data to constitute prior art. Thus, in the view of the consortium, derivation of haplotypes and "haplotype tag SNPs" from HapMap data should be considered obvious and thus not patentable. Therefore, the original reasons for imposing the licensing requirement no longer exist and the requirement can be dropped. This decision will allow the HapMap project's Data Coordination Center to post all of the consortium's monthly release of data and to distribute this data to other public databases, such as the NIH-funded National Center for Biotechnology Information's dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/) and the JSNP Database in Japan (http://snp.ims.u-tokyo.ac.jp/).
"We are excited that the HapMap data will be even more easily available for researchers to use in their efforts to find genes that influence many common diseases, such as diabetes, hypertension and arthritis. Gene mappers have been using the HapMap data almost as rapidly as we have been able to generate them," said Yusuke Nakamura, M.D., Ph.D., director of the University of Tokyo's Human Genome Center, as well as leader of the RIKEN SNP Research Center and the Japanese group working on the International HapMap Project.
Researchers are already using the HapMap data to study conditions such as type 2 diabetes, asthma and dyslexia, as well as genes related to differences in how individuals metabolize and react to certain medications. When the HapMap is completed next year, those studies will be able to be carried out even more efficiently.
"We are delighted that our public databases will now be able to integrate the HapMap data with other genomic data," said Ewan Birney, Ph.D., who heads Ensembl, one of the public databases that had been unable, until today, to incorporate the HapMap data, and which is a joint genome browser project between the European Bioinformatics Institute and the Wellcome Trust Sanger Institute in Cambridge, England. "Now, researchers will be able to study how this new information about human genetic variation relates to genes and their function. Such studies are essential to efforts to develop better ways of diagnosing, treating and preventing human disease."
Source: Eurekalert & othersLast reviewed: By John M. Grohol, Psy.D. on 21 Feb 2009
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