October 26, 2005
Human Genetic HapMap Phase I Published

The human geonome Haplotype Map (HapMap) project has reached an important milestone.

At the project's outset in October 2002, the consortium set an ambitious goal of creating a human haplotype map, or HapMap, within three years. The Nature paper marks the attainment of that goal with its detailed description of the Phase I HapMap, consisting of more than 1 million markers of genetic variation, called single nucleotide polymorphisms (SNPs). The consortium is also nearing completion of the Phase II HapMap that will contain nearly three times more markers than the initial version and will enable researchers to focus their gene searches even more precisely on specific regions of the genome.

Identification of locations where chromosomes swap sections of genetic code provides a number of benefits. One big advantage is that it allows testing of smaller numbers of locations in order to better guess what sequence variations will be found at untested locations. This lowers the cost of genetic testing. This is great for tracking which genetic sequence variations are correlated with specific diseases, physical body shapes and colors, and cognitive differences among other areas of human differences.

Just because most people who have particular SNPs at particular locations usually also then have particular other SNPs at other locations does not mean this is always the case. Some people will have rarer mutations (in fact we probably all have unique mutations). So the coming decline in cost of DNA sequencing by orders of magnitude will provide useful benefits, especially for identifying rarer mutations and identifying who has those rarer mutations.

Identification of the key SNP locations also provides a sort of roadmap for the study of human evolution. The fact that some sections with common sets of SNPs are shorter and other sections are longer is helpful in identifying genetic functionality that has been under a great deal of selective pressure.

Genetic diversity in humans is increased by recombination, which is the swapping of DNA from the maternal and paternal lines. It has been recently realized that in humans, most such swapping occurs primarily at a limited number of "hotspots" in the genome. By analyzing the HapMap data, the researchers have produced a genome-wide inventory of where recombination takes place. This will enable more detailed studies of this fundamental property of inheritance, as well as serve to improve the design of genetic studies of disease.

The scientists found evidence of selective pressures for both immune response and cognitive function.

The HapMap consortium found that genes involved in immune response and neurological processes are more diverse than those for DNA repair, DNA packaging and cell division. Researchers speculate the difference might be explained by natural selection shaping in the human population in ways that favor increased diversity for genes that influence the body's interactions with the environment, such as those involved in immune response, and that do not favor changes in genes involved in core cellular processes.

As expected, the vast majority of both rare and common patterns of genetic variation were found in all of the populations studied. However, the consortium did find evidence that a very small subset of human genetic variation may be related to selection pressures related to geographic or environmental factors, such as microorganisms that cause infectious diseases. This evidence appears as significant differences in genetic variation patterns in particular genomic regions among the populations studied. While more follow-up study is needed to explore the differences, researchers say some of the most striking examples merely serve to confirm well-known genetic differences among populations, such as the Duffy blood group, which plays a role in response to malaria, and the lactase gene, which influences the ability to digest milk products.

In 20 or 30 years most of the selective pressures that acted on the human race in local environments will probably be well characterised and their effects quantified down at the level of frequencies of genetic variations in different human populations. We are living in the final years of our ignorance of how natural selection molded humans to produce the wide range of human variations we see today.

The HapMap is for single point mutations. But recent progress in identifying larger scale structural variations such as large copy variations is starting to paint a picture of much larger amounts of genetic variation between individuals and groups.

Share |      Randall Parker, 2005 October 26 03:17 PM  Trends, Human Evolution

PacRim Jim said at October 26, 2005 9:27 PM:

Anyone want to swap SNPs?

Dave Schuler said at October 27, 2005 11:21 AM:

Problems with your trackbacks, so ping!

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