SAN DIEGO ¿ The U.S. leaders of the human genome project, Francis Collins and Craig Venter, announced plans for the next public/private collaborative project in genomics ¿ a haplotype map.

Speaking at the BIO 2001 conference in San Diego last week, Collins said the project will be formalized at a meeting of industry representatives and academics later this month. The overall aim is to produce a map of genetic variations between individuals as a tool for pharmacogenomics. ¿Haplotypes are a tricky concept in population genetics but they are going to be a very powerful tool,¿ Collins said.

Haplotypes are groups of single nucleotide polymorphisms (SNPs), typically covering 60,000 base pairs that tend to be inherited together. This means that they promise to provide a more focused and manageable tool for pharmacogenomics than analyzing the 2 million to 3 million SNPs in the genome.

¿It is like the difference between buses and cars,¿ said Venter. ¿Between any two individuals you find only a few thousand changes [SNPs], maybe 10,000 linked to a biological outcome.¿ Less than 1 percent of SNPs occur in coding regions of the genome.

Using his own specialty of diabetes to illustrate the power of this approach, Collins said, ¿If you wanted now to take 100 diabetics and 100 nondiabetics and find the dozen genetic variants that contribute to diabetes, you would theoretically have to look at millions of SNPs, but much of that would be redundant data. This is a way to pick out the minimal set of SNPs that you need. You would save yourself about two orders of magnitude of work.¿

However, there are significant technical obstacles. For example, creating the haplotype map will require extremely accurate genotyping equipment as it will involve scoring at least 20 SNPs at a time, and errors could add up.

One of the leading companies in the field of haplotyping, Genaissance Pharmaceuticals, of New Haven, Conn., working in collaboration with the University of Cincinnati, said in September 2000 that it had identified 12 haplotypes that influenced patients¿ response to the asthma drug albuterol.

Collins said, ¿The suggestion is, within two years as a public project, with the support of the pharmaceutical industry, we could do it.¿

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