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SNPs HapMap genotyping completed; data analysis coming soon

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It was somehow fitting that the year’s major HapMap announcement came in a city known for its leading family history data resources. In Salt Lake City last fall, 21 representatives of the International HapMap Project led a press conference to announce the completion of the first phase of the project.

That first phase — genotyping and analysis of 1 million samples from more than 250 people across four populations — culminated in the deposit of all of that data into the public domain in late October. At the press conference, Kelly Frazer from Perlegen was on hand to announce another landmark: all of the genotyping for phase II, this one including 2.1 million SNPs, had also been finished. She said analysis would be performed during “the next few months.” And with that, the HapMap project will officially be done.

The project, which sprang from its first strategy meeting in October 2002, has led to a HapMap “three times more detailed than what we thought would be possible,” said NHGRI Director Francis Collins at the event. “Now we can use it to find virtually any heritable cause of virtually any common disease.”

David Altshuler, representing the Broad Institute, added some balance to the back-patting, warning that “much additional work is needed to confirm and extend these findings.”

Among the key findings of the HapMap are a series of what scientists are calling “tag SNPs” — single SNPs that can stand as a proxy for an entire haplotype. Another accomplishment of the effort, added Perlegen’s Frazer, was an overall cost reduction in genotyping technology “on the order of two magnitudes.”

Looking ahead, scientists expect to do a lot of research to validate the HapMap results, especially in broader populations. Presenter Charles Rotimi from Howard University said his group planned to test the haplotypes found through the collaboration in seven new populations. Genotyping for those, he said, would begin this spring or summer.

Translating this to improved medicine will be tricky, presenters agreed. “The challenge is to take these observations and turn them into” clinically relevant tools, said Collins. HHS Secretary Michael Leavitt said new targeted therapeutics would not gain wide use without “reinvent[ing] the regulatory systems.”

— Meredith Salisbury
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