HapMap Project allows data to be published in other databases.
To the delight of researchers mining the human genome for disease-related genes, restrictions on the use of data from the International HapMap Project were dropped last week. The information can now be incorporated into other databases, allowing easy access for scientists around the globe.
Researchers seeking the genetic component of a specific disease are interested in single nucleotide polymorphisms (SNPs) — points in the genome where one base often differs between individuals. But there are an estimated ten million common SNPs, so it is quicker to search for common haplotypes linked to a disease — larger blocks of DNA that are often inherited together. The HapMap project is a consortium of some 25 groups, which have been collecting data on haplotypes since October 2002.
When the US$100-million project began, organizers were worried that people would mine the data and attempt to patent haplotypes. So users had to agree not to limit access to the information, for example by patenting it, and not to share the data with anyone who hadn't made the same agreement.
But this had the unfortunate side effect that data could not be integrated into large, open-access genomic databases such as Ensembl. “We could pick up the data and do a lot of analysis, but we couldn't give it back to anyone,” says bioinformatician Ewan Birney, who heads Ensembl.
Those restrictions have now been lifted. Birney predicts that the increase in Ensembl data will throw up haplotypes for diseases such as Alzheimer's, diabetes or heart disease within the next two years. “It will switch on the light,” he says. “For some diseases, major risk factors will be discovered.”
HapMap partners hope that haplotypes related to specific diseases will be commercialized, says Lisa Brooks, a director of the US Genetic Variation Program, but that basic haplotype information will remain freely available. Brooks adds that enough data and analysis are now public that claims of novelty needed to secure a patent should be difficult to prove.