snp
single nucleotide polymorphisms (SNPs, pronounced "snips"), which can be used in characterizing drug responses. The National Institutes of Health has launched a $36-million, three-year program to collect data on 50,000 to 100,000 SNPs, a new goal for its Human Genome Project. The information would be used not only to gauge drug responses but also to study disease susceptibility and to conduct basic research on population genetics. In midsummer a group of pharmaceutical companies discussed forming a consortium with the NIH that would supply additional funding and research resources to create an even larger public database. One impetus to establish a tie with industry has been a concern that private attempts to patent SNPs could choke off access to data for basic research. "These research tools are far upstream of any particular product," notes Francis S. Collins, who oversees the Human Genome Project at the NIH. "The public is best served by having them accessible to any researcher who wants to use them."
A pharmaceutical industry collaboration with the NIH would promote public access to SNPs. Still, some biotechnology companies have rushed to embrace pharmacogenomics by creating private databases. A French company, Genset, is testing the DNA of more than 100 people to develop a map of the entire human genome. The Genset map will contain 60,000 SNPs that are within or near genes that cause disease or differing drug reactions. Genset's chief genomics officer, Daniel Cohen, devised the first rough physical map of the human genome in 1993.
Abbott Laboratories, a major U.S. pharmaceutical manufacturer, has invested $20 million in Genset. The companies will market SNP map data to drug companies that wish to pinpoint during clinical trials a common set of variant nucleotides shared by people who do not respond to a drug. This information could then be used to create diagnostic tests to filter out unresponsive patients. Abbott, in fact, is paying Genset an additional $22.5 million to help it develop a diagnostic test to screen patients for zileuton, its own asthma drug, which can induce liver toxicity in 3 percent of patients. Genset is not the only one putting together SNP databases. In August, Incyte Pharmaceuticals announced plans to purchase Hexagen in Cambridge, England, as part of its effort to detect genetic variation.
The application of rapid tools for screening SNPs may eventually make it possible to look for the unique signature of an individual's DNA in a matter of hours. Traditional gene-sequencing technology might take two weeks and $20,000 to screen a single patient for variations in 100,000 SNPs. "That's going to make this prohibitive to put into a clinical-trial kind of system," noted Robert Lipshutz of DNA chipmaker Affymetrix at the annual meeting of BIO, a biotechnology industry trade group. Affymetrix is testing a chip that can detect 3,000 SNPs in less than 10 minutes. As the technology progresses, Affymetrix expects to be able to mill through 100,000 SNPs dispersed through a patient's genome in several hours, for as little as a few hundred dollars. |
