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A little variation is the spice of life: SNPs
By Bijal P. Trivedi

Human beings are remarkably similar. We all share about 99.9 percent of the same genetic sequence regardless of ethnicity. However, within the human species as a whole there are likely to be millions of tiny variations. Within a portion of these variations lies the genetic basis for susceptibility to a range of diseases like cancer, heart disease, diabetes or Alzheimer's. In the current issue of Science, scientists at Celera Genomics report 2.1 million Single Nucleotide Polymorphisms (SNPs), the most common type of variation in the genome. The challenge now is to understand how each variation affects human health or disease.

Of the 2.1 million SNPs, less than one percent, or around 21,000, are found in genes. SNPs within genes are the most interesting to researchers because these are the ones that are most likely to affect proteins. SNPs found in the regulatory region outside of a gene have the potential to affect when and how the gene is turned on, which affects the quantity of the protein produced. SNPs found within the gene can produce deleterious structural changes in the protein that prevent it from doing its job in the cell, leading to disease.

But all SNPs are useful, even those not located in the vicinity of a gene. Celera scientists report SNPs occur approximately every 1250 bases, making them valuable genetic markers for locating disease-causing genes. Almost every week marks the publication of a newly identified SNP that has been associated with one disease or another. Recent reports have identified SNPs associated with severe ulcerative colitis, Alzheimer's and increased risk of HIV infection. SNPs that are associated with a particular disease are potentially valuable as diagnostic markers for determining a person's risk of developing certain conditions.

The International SNP Map Working Group (ISMWG) has identified 1.42 million SNPs, which occur about every 1900 bases. These results are published in this week's Nature.

The complete human sequence offers scientists the first opportunity to harvest a genome-wide crop of SNPs that shows how variation is scattered around the genome. To their surprise, Celera scientists found that SNPs are not evenly distributed. For reasons that are not understood, there appear to be hotspots for variability which are SNP-rich, and vast regions between genes that are SNP-poor. The ISMWG found that the amount of variation was substantially less in X and Y chromosomes. They also identified a hotbed of variation nestled in the HLA region that contains genes vital to our immune response.

Geneticists, physicians, and pharmaceutical companies are not the only ones who stand to gain from SNPs. Anthropologists will be able harness genetic clues and use SNPs to trace the emergence of different populations and their migrations throughout the world.

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Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (February 15, 2001).
Venter, J.C. et al. The sequence of the human genome. Science 291, 1304-1351 (February 16th, 2001).

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