second-generation database discussed in Nature contains 3.1 million SNPs, three times more than Phase I.

The International HapMap Consortium published analyses of its second-generation map of human genetic variation in the October 18 issue of Nature. This haplotype map, or Phase II HapMap, contains more than 3.1 million SNPs, three times more than the approximately 1 million SNPs contained in the initial version.

Researchers can access the Phase II map data through the HapMap Data Coordination Center, the National Center for Biotechnology Information’s dbSNP, and the JSNP Database in Japan.

The Phase II HapMap was produced using the same DNA samples from the Phase I HapMap. That DNA came from blood collected from 270 volunteers from four geographically diverse populations: Yoruba in Ibadan, Nigeria, Japanese in Tokyo, Han Chinese in Beijing, and Utah residents with ancestry from northern and western Europe.

To provide information on less common variations and to enable researchers to conduct genome-wide association studies in additional populations, NHGRI plans to extend the HapMap even further. Among the populations donating additional DNA samples are Luhya in Webuye, Kenya, Maasai in Kinyawa, Kenya, Tuscans in Italy, Gujarati Indians in Houston, Chinese in Denver, people of Mexican ancestry in Los Angeles, and individuals of African ancestry in southwestern US.

According to the consortium’s overview paper, the Phase II HapMap found a surprising extent of recent common ancestry in all of the population groups. They also say that it enabled researchers to more precisely quantify the rates of shuffling seen among different gene classes in the human genome.

The recombination rates reportedly vary more than sixfold among different gene classes. The highest rates were found among genes involved in the body’s immune defense, while the lowest appear among genes for chaperones, according to the researchers. In general, genes that code for proteins associated with the surface of cells and external functions such as signaling were found to be more prone to recombination than those that code for proteins inside cells.

Another paper appearing in the same issue of Nature describes how the enhanced map can help pinpoint pivotal changes in the human genome that arose in recent history.

This study also identified DNA variations in African populations that may be linked to resistance to Lassa fever. These changes lie in two genes, LARGE and DMD, which are involved in viral entry into cells.

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