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Collins and Venter Hint at Haplotype Mapping Initiatives

SAN DIEGO, June 27 - Hap maps are coming. Francis Collins said in a speech at the BIO 2001 meeting in San Diego today that a haplotype map could be the next undertaking of the National Human Genome Research Institute. Collins said early-stage planning is underway for a public-private collaboration to build a database identifying “blocks” of base pairs containing variants linked to inherited diseases. 

In a separate remark to GenomeWeb, Craig Venter, who was honored along with Collins at the meeting as the recipient of the Chemical Heritage Society’s biotechnology award, said that Celera would not participate in such a consortium but would soon announce a haplotype project of its own. 

Collins said that early-stage plans for a public-private haplotype map project would be hashed out during a July 18-19 workshop at the National Institutes of Health (NIH). The map would provide insight into markers for common inherited diseases by identifying blocks or neighborhoods of up to 60,000 base pairs that contain groups of SNPs associated to disease. For instance, Collins explained that a neighborhood of base pairs containing a gene involved in diabetes would likely contain other common variants that could predict the presence of SNPs related to diabetes. A haplotype map could save “two orders of magnitude of work” in researching such diseases, Collins said.  

Although the scientific approach for genotyping and scoring the DNA sets that would make up such a map has yet to be selected, Collins predicted that, with collaboration among public and private sector groups, it could be generated in a couple of years. 

Collins told GenomeWeb that a paper on linkage disequilibrium published recently in Nature by Eric Lander and others was the catalyst for a haplotype map project. The paper showed that the size of blocks of base pairs containing related SNPs in the human genome are significantly larger than previously believed—that chunks of as many as 60,000 base pairs instead of just 3,000 are commonly inherited in unbroken form. Collins said that Lander’s group at the Whitehead Institute Center for Genome Research, David Bentley’s group at the Sanger Center, and the Wellcome Trust have already expressed serious interest in a haplotype map project. 

The hap map is the most recent addition to a list of public/private genomics efforts under discussion at NIH. “There is a lot of enthusiasm for this [public-private] model,” Collins told GenomeWeb. Other joint projects being considered include a structural genomics consortium, a “flexgene” project that would look at full-length cDNAs in expression vectors, a fungal genome project, a gene expression array database project, and further collaborations on the mouse genome. 

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