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HapMap Consortium Publishes 'Phase II' Genetic Variation Map with 3M SNPs

NEW YORK (GenomeWeb News) – The International HapMap Consortium this week published a new version of its map of human genetic variation, which includes more than 3.1 million SNPs -- three times more than the initial version of the map published in 2005.
 
The higher-resolution Phase II haplotype map “offers greater power to detect genetic variants involved in common diseases, explore the structure of human genetic variation, and learn how environmental factors, such as infectious agents, have shaped the human genome,” said the National Human Genome Research Institute, which led the US component of the project.
 
An overview paper outlining the Phase II findings and another related study using HapMap were published in this week’s issue of Nature.
 
The overview paper shows "the surprising extent of recent common ancestry found in all of the population groups" involved in the study, NHGRI said.
 
Both phases of the HapMap project used blood collected from 270 volunteers from Nigeria, Japan, Beijing, and Utah. The consortium estimates that the Phase II HapMap includes between 25 percent and 35 percent of common genetic variation in these populations.
                                                                                           
Analysis of these samples showed that between 10 percent and 30 percent of the DNA segments from each representative population shared regions that signaled descent from a common ancestor within 10 to 100 generations.
 
NHGRI said the counterpart study describes how the new map can be used to "pinpoint pivotal changes in the human genome that arose in recent history." These changes became common through natural selection, which means "they were somehow beneficial to human health," but for the time being "their biological significance remains largely unknown."
 
The gene variants identified in the study “open new windows on these evolutionary forces and provide a launching point for future biological studies of human adaptation," said first author Pardis Sabeti, a postdoc fellow at the Broad Institute of MIT and Harvard.
 
The HapMap program will be expanded in the future to include samples from other populations, including Luhya and Maasai in Kenya, Tuscans in Italy, Gujarati Indian in Houston, Chinese in metropolitan Denver, and people of Mexican ancestry in Los Angeles.
 
The project to date has been a collaborative effort from scientists and funding agencies in Japan, the US, the UK, Canada, China, and Nigeria.
 
NHGRI said the development of the new HapMap "relied heavily on the high-throughput genotyping capacity of Perlegen Sciences," which "tested virtually the entire known catalog of human SNP variation" and "contributed some of its own resources to make the map possible."
 
Further information about the HapMap project is available here.