The United States National Institutes of Health recently announced its involvement in funding several organizations, including the Johns Hopkins McKusick-Nathans Institute of Genetic Medicine, for the international effort to map the human genome. Focusing on gene sequences in genetically induced diseases, the project is dubbed the "International HapMap Project," and involves both public and private institutions in the United States, Canada, the United Kingdom, China, Japan and Nigeria.
Aravinda Chakravarti, Ph.D., and the director of the McKusick-Nathans Institute, will lead the Hopkins team in conjunction with researchers at the University of California, Baylor College of Medicine and the Whitehead Institute for Biomedical Research to analyze the 31 percent of the human genome.
The Beijing Genomic Institute and The China HapMap Consortium, funded by the Chinese Ministry of Science and Technology, the Chinese Academy of Sciences, and the Natural Science Foundation of China, will analyze 10 percent of the genome. Scientists at McGill University in Canada plan to also analyze 10 percent of the genome, The University of Tokyo will analyze 25 percent of the genome, and the United Kingdom will analyze 24 percent of the genome, with funding and work done by the Wellcome Trust, at their Sanger Institute and Centre for Human Genetics.
The project, expected to take three years, will compare the gene sequences of various individuals sampled from genetic populations from Nigeria, China, Japan and Europe, and its findings will be continuously released on the Internet for access by other scientists.
Central to the research is the idea of genetic similarity. Presently, research shows that any two people are 99 percent genetically similar, while the other one percent accounts for variation between humans and therefore explains all the differences ranging from immune systems to hair color.
The actual genome to be studied is made up of strands of deoxyribonucleic acid (DNA) and is encoded by four chemicals, called nucleotides that vary from link to link down the DNA chain. The four nucleotides found in any genetic sequence are adenine, cytosine, guanine and thymine, and the order in which they occur dictates the physiological characteristics of the individual.
When one of the four nucleotides in a sequence is replaced by another, the basic instructions for the life form are changed and result in single nucleotide polymorphisms (SNPs). Approximately three million of these SNPs have already been studied and compiled in an online database called DBSNP.
It is believed that over 10 million SNPs exist in humans, and the task of finding and cataloging all SNPs will be laborious. Those involved with the HapMap Project believe their task to be more feasible because they will not be analyzing all individual SNPs found in the human genome. Their task involves identifying DNA aggregates in the genome chain where groups of related SNPs can be identified.
Called haplotypes (thus the name HapMap), these aggregates can be identified because they are inherited together, and occur in certain patterns in the same DNA chain.
"We expect these genetic Ochunks' to hold clues about the subtle genetic influences that result in complex diseases, illnesses in which genes and environment are involved," says Aravinda Chakravarti, Ph.D., director of the McKusick-Nathans Institute, in a recent interview for a Hopkins Medical School press release.
"Since it's clear that more than one gene contributes to these diseases, we need to have a snapshot of multiple genes, their usual sequences and their common variations. The haplotype map will give us that big picture."
Due to the fact that all human DNA stems from a relatively small population from Africa, there are few differences in the basic human DNA sequence, with similar variances from the original pattern shared in current populations. It is believed that in order to identify each group of related SNPs, only a few tagged SNPs will be needed to analyze each related group.
Once the HapMap has been completed, researchers will compare the DNA of people with a certain disease to the DNA to those without it, and the differing haplotypes will consequently be identified and studied. Aside from the main purpose of disease research, the completed HapMap can be used to advance study in many other genetically affected fields.
Pharmaceutical companies, for example, could use the HapMap to identify a gene sequence common to certain populations and consequently upgrade their drug to have fewer side effects.
With over 100 million dollars in grants, this project is expected eventually help locate the genetic variations that contribute to good health, such as an immunity against infectious diseases or the promotion of longevity.
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