On Oct. 17, 2007, the International HapMap Consortium published analyses of its second-generation map of human genetic variation, which contains three times more markers than the initial version unveiled in 2005. In two papers in the journal Nature, the consortium describes how the higher resolution 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.

Any two humans are more than 99 percent the same at the genetic level. However, it is important to understand the small fraction of genetic material that varies among people because it can help explain individual differences in susceptibility to disease, response to drugs or reaction to environmental factors. Variation in the human genome is organized into local neighborhoods called haplotypes, which usually are inherited as intact blocks of information. Consequently, researchers refer to the map of human genetic variation as a haplotype map, or HapMap.

The International HapMap Consortium is a public-private partnership of researchers and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States. The U.S. component of the project is led by the National Human Genome Research Institute (NHGRI) on behalf of the 20 institutes, centers and offices of the National Institutes of Health (NIH) that contributed funding.

The second-generation haplotype map, or Phase II HapMap, contains more than 3.1 million genetic variants, called single nucleotide polymorphisms (SNPs) – three times more than the approximately 1 million SNPs contained in the initial version. The more SNPs that are on the map, the more precisely researchers can focus their hunts for genetic variants involved in disease. The rapid growth of genome-wide association studies over the past year and half has been fueled by the HapMap consortium’s decision to make its SNP datasets immediately available in public databases, even before the first and the second versions of the map were fully completed.

Researchers around the globe have now associated more than 60 common DNA variants with risk of disease or related traits, with most of the findings coming in the past nine months. As just one example, the Wellcome Trust consortium in England looked at 14,000 cases and 3,000 shared controls, finding variants associated with increased risk of bipolar disorder, coronary artery disease, Crohn’s disease, rheumatoid arthritis, type 1 diabetes and type 2 diabetes.