The INDIVIDUALIST

A Wiki about biochemical individuality

Genomics

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Description

Single nucleotide polymorphisms or SNPs (pronounced "snips") are DNA sequence variations that occur when a single nucleotide (A,T,C,or G) in the genome sequence is altered. For example a SNP might change the DNA sequence AAGGCTAA to ATGGCTAA. For a variation to be considered a SNP, it must occur in at least 1% of the population. SNPs, which make up about 90% of all human genetic variation, occur every 100 to 300 bases along the 3-billion-base human genome. Two of every three SNPs involve the replacement of cytosine (C) with thymine (T). SNPs can occur in both coding (gene) and noncoding regions of the genome. Many SNPs have no effect on cell function, but scientists believe others could predispose people to disease or influence their response to a drug.

Although more than 99% of human DNA sequences are the same across the population, variations in DNA sequence can have a major impact on how humans respond to disease; environmental insults such as bacteria, viruses, toxins, and chemicals; and drugs and other therapies. This makes SNPs of great value for biomedical research and for developing pharmaceutical products or medical diagnostics. SNPs are also evolutionarily stable --not changing much from generation to generation --making them easier to follow in population studies.

Scientists believe SNP maps will help them identify the multiple genes associated with such complex diseases as cancer, diabetes, vascular disease, and some forms of mental illness. These associations are difficult to establish with conventional gene-hunting methods because a single altered gene may make only a small contribution to the disease.

Several groups worked to find SNPs and ultimately create SNP maps of the human genome. Among these groups were the U.S. Human Genome Project (HGP) and a large group of pharmaceutical companies called the SNP Consortium or TSC project. The likelihood of duplication among the groups was small because of the estimated 3 million SNPs, and the potential payoff was high.

In addition to the pharmacogenomic, diagnostic, and biomedical research implications, SNP maps are helping to identify thousands of additional markers along the genome, thus simplifying navigation of the much larger genome map generated by researchers in the HGP.

Discussion

How can SNPs be used as risk factors in disease development?

SNPs do not cause disease, but they can help determine the likelihood that someone will develop a particular disease. One of the genes associated with Alzheimer's, apolipoprotein E or ApoE, is a good example of how SNPs affect disease development. This gene contains two SNPs that result in three possible alleles for this gene: E2, E3, and E4. Each allele differs by one DNA base, and the protein product of each gene differs by one amino acid.

Each individual inherits one maternal copy of ApoE and one paternal copy of ApoE. Research has shown that an individual who inherits at least one E4 allele will have a greater chance of getting Alzheimer's. Apparently, the change of one amino acid in the E4 protein alters its structure and function enough to make disease development more likely. Inheriting the E2 allele, on the other hand, seems to indicate that an individual is less likely to develop Alzheimer's.

Of course, SNPs are not absolute indicators of disease development. Someone who has inherited two E4 alleles may never develop Alzheimer's, while another who has inherited two E2 alleles may. ApoE is just one gene that has been linked to Alzheimer's. Like most common chronic disorders such as heart disease, diabetes, or cancer, Alzheimer's is a disease that can be caused by variations in several genes. The polygenic nature of these disorders is what makes genetic testing for them so complicated.

References

Genetic interactions with diet influence the risk of cardiovascular disease.

Am J Clin Nutr. 2006 Feb;83(2):443S-446S. Ordovas JM.

  • Single-nucleotide polymorphisms are an integral component of the evolutionary process that over millennia have resulted from the interaction between the environment and the human genome. Relatively recent changes in diet have upset this interaction with respect to the nutritional environment, but nutritional science is beginning to better understand the interaction between genes and diet, with the resulting potential to influence cardiovascular disease risk by dietary modification. Single-nucleotide polymorphisms in several genes have been linked to differential effects in terms of lipid metabolism; however, even a simple model of benefit and risk is difficult to interpret in terms of dietary advice to carriers of the various alleles because of conflicting interactions between different genes. The n-3 family of polyunsaturated fatty acids is underrepresented in our modern diet; much of the benefit of polyunsaturated fatty acids found in studies of various polymorphisms seems to be linked to increased n-3 polyunsaturated fatty acid intake. The nascent science of nutrigenomics faces many challenges; more and better research is needed to clarify the picture, rebut scepticism, and re-invigorate the discussion concerning genetic polymorphism and its interaction with diet.

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