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This is Part 2 of a two-part story on the science and promise of the International HapMap Project. Part 1 was published on November 7.

Sequencing a single human genome took an international team comprising hundreds of researchers 13 years. Now, in just three years, another global consortium has begun to identify the genetic differences among hundreds of individuals from four countries – and fashion them into a powerful new tool for understanding how these differences affect human health.

The International HapMap Project, launched in October 2002, has catalogued more than three million single-nucleotide polymorphisms (SNPs), or single-point differences in the sequence of the human genome, based on samples from four different populations around the world. More than 200 scientists in Canada, China, Japan, Nigeria, the United Kingdom, and the United States participated in the project. The team published an analysis of the project’s first phase, examining about one million of those variations, in the October 27 issue of Nature.

The study reported on genetic differences identified in 269 individuals: 90 from the Yoruba in Ibadan, Nigeria; 90 from Utah, representing people of northern European ancestry; 45 Han Chinese from Beijing, China; and 44 Japanese from Tokyo, Japan. These differences are inherited in large blocks, called haplotypes. The data analysis was led by Peter Donnelly of the University of Oxford in England and David Altshuler, director of the program in Medical and Population Genetics of the Broad Institute of Harvard and MIT in Cambridge, MA.

The HapMap Consortium undertook the project in an effort to speed the identification of genes involved in common diseases, such as cancer and diabetes. “The goal in this project is a medical one: we want to advance medical genetic studies of disease, and we want to do this in a way that would benefit people throughout the world,” says Mark J. Daly, who led the Broad Institute’s analysis efforts for the HapMap.

Different populations have haplotype blocks of different lengths, and may also inherit different patterns of variation, making the decision to study diverse populations inevitable. With a full catalog of haplotype patterns, researchers can speed up their hunts for disease-related genes by selecting “tag SNPs,” individual variations that depict the full pattern of differences in each block.

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