There are about 10 million common SNPs in the human population. Scanning the genomes of large numbers of patients for such a large number of variants would be prohibitively expensive. Fortunately, a major shortcut has been discovered that reduces the workload about 30-fold. The International HapMap Project, led by the NIH and completed in October 2005, demonstrated that the 10 million variants cluster into local neighborhoods, called haplotypes, and that they can be accurately sampled by as few as 300,000 carefully chosen SNPs. New technological systems allow these SNPs to be systematically studied in high-throughput facilities that dramatically lower the cost.
For each study of 1,000 to 2,000 patients with a specific disease and a similar number of people who do not have the illnesses (controls), an investment of $3 million to $6 million (depending on the number of patients and controls) is needed for the first stage of genotyping. Follow-up studies to validate the results with additional patients and controls, data analysis, and patient management expenses will add to these basic costs. It is important to note, however, that these costs are a small fraction of what has already been invested in enrolling these study subjects, examining them, carrying out extensive laboratory investigations, and collecting their DNA.
The genotyping work itself will be performed by either commercial or government laboratories. The initial GAIN genotyping supported by Pfizer will be carried out by Perlegen Sciences, Inc., of Mountain View, Calif., and will start in late summer 2006; Pfizer is contributing these Perlegen-produced genotypes as an "in kind" donation to the project. A simil
Source:NIH/National Human Genome Research Institute