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Following the Data

In his small office in a corner of a busy research lab at Boston’s Massachusetts General Hospital, David Altshuler, a physician and expert on diabetes, is full of restless energy. Six floors below, gridlock has brought the traffic coming in and out of the sprawling hospital to a maddening halt. But Altshuler, who is also the director of medical and population genetics at the Whitehead Institute and a prime mover behind the HapMap project, can barely sit still. The critics of the HapMap in the genetics community clearly have him peeved.

“They’re nihilists. All they say is, Don’t do it.’ I don’t believe it’s a panacea, but it’s a useful tool,” says Altshuler. He points to the failure of many critics to propose a feasible alternative as particularly frustrating. “Ultimately, all of genetics boils down to measuring the genetic variation in some population of people and comparing it to their characteristics and looking for correlations. That’s all genetics ever is.” And, adds Altshuler, the HapMap “is simply a tool to study genetic variation at unprecedented levels of accuracy and detail.”

Altshuler freely acknowledges that many scientific questions remain about how genes vary among individuals and populations and even about how effective looking at patterns of common genetic variations will be in tracking down risk factors for diseases. But, he adds, the HapMap offers a direct route to testing ideas about the genetics of common diseases. “For that reason alone,” he says, “it is an important investment.”

One issue to be resolved is how extensively human populations share specific versions of haplotype blocks. Geneticists do know that some differences between populations are a consequence of their migrational history. They expect, for example, that the length of haplotype blocks in populations from Africa will be shorter than those in populations of European or Asian origin. That’s because humans originated in Africa and migrated throughout the rest of the world, starting around 50,000 years ago. Thus, the genetic history of populations in Africa is older and, since their genes have had a far longer time to vary, the linked blocks have had more of a chance to break up into smaller segments. It is also likely that any migration out of Africa did not include representatives from all groups, so geneticists expect to find more diversity in Africa.

Altshuler and his colleagues found strong evidence that this is precisely the case in a preliminary study they did of the haplotype patterns of nearly 300 people, including African Americans, people from Nigeria, and volunteers with European, Japanese, and Chinese ancestry. In a paper published last summer in the journal Science, the researchers described finding most of the common haplotype varieties in all the populations, though samples from Africa showed the greatest diversity and also tended to have shorter haplotype segments. The paper’s conclusion: while there are some differences, the boundaries of the haplotype blocks and the common versions are largely shared across populations.

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Tagged: Biomedicine, geneology, copy number variation

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