Genetic Testing & Health: SNPs
Single nucleotide polymorphisms (SNPs) are genetic mutations that affect the functioning of genes that maintain cells, alter how the body uses nutrients, and are believed to increase the likelihood of acquiring certain diseases. SNPs also can affect how well the body absorbs various nutrients, including vitamins A and D, iron, and lipids.
Run-of-the-mill genetic testing will uncover some of the SNPs that are known and at least partially understood but the company doing the testing may not share that information with you as part of the results. To understand more about this emerging field and how it may impact you, there are secondary tools that may be helpful. But first, make sure you understand what these small genetic aberrations are and how they may impact you.
A Closer Look at SNPs
SNPs comprise 90 percent of all variations in the human genome and involve substituting one base for another at a specific location. Because there are four nucleotides — A, C, G, and T — a given SNP can have up to four versions. For a single-nucleotide substitution to be considered an SNP, two or more versions of a particular genetic sequence must both be found in at least 1% of the general population. That said, SNPs are relatively common in the human genome, occurring in about one out of every 300 base pairs of nucleotides. Because the human genome contains about 3 billion nucleotides, that means each person’s individual genome contains about 10 million SNPs.[4, 5, 6, 7]
Although some SNPs have been associated with various diseases — such as rheumatoid arthritis, thyroid cancer, and diabetes — SNPs comprise a much broader category of genetic mutations than mutations that cause, or might cause, diseases.[8, 9, 10] That’s because SNPs don’t always occur in the parts of a gene that govern how proteins are coded or now they function. Rather, SNPs can be located in other parts of a gene that don’t affect proteins, or outside of genes entirely. And even if an SNP isn’t located within a gene, it can help scientists determine which genes are associated with a particular disease.
In summary, although most SNPs don’t affect a person’s health, some of them can be useful in predicting individual reactions to various nutrients, drugs, and environmental toxins, as well as a person’s risk of acquiring certain conditions.[4, 5, 6, 7]
DNA methylation is one of several ways that cells control gene expression by turning off various genes. Currently, scientists are not certain exactly how this process works. However, DNA methylation is crucial for proper cell differentiation and the development of embryos. Moreover, studies have shown that methylation that occurs near a gene promoter — part of a DNA sequence that starts the transcription process for a certain gene — can vary depending on what kind of cell is involved. Methylation levels also vary between different types of tissue.
How SNPs Affect Nutrient Needs
SNPs can alter how a person absorbs and metabolizes various nutrients, such as lipids and vitamins. They do this primarily by affecting DNA methylation patterns and thus influencing gene expression in response to these nutrients. Many dietary constituents affect post translation events and many account for at least part of the variation in response to the dietary components.
One of the most common SNPs is the C677T polymorphism of the methylenetetrahydrofolate reductase (MTHFR) gene, which causes that gene to produce its associated enzymes at a slower rate. In a person with C677T, the result is that their ability to use folate to regulate gene expression and perform other important functions is impaired. The same SNP may increase the body’s product of the type of folate used to make thymidine (the “T” in a DNA sequence). As as a result, people who carry this SNP and don’t get enough folate in their diet may be more more susceptible to developmental defects.[2, 5] Other SNPs have been found to affect folate uptake as well.[11, 13]
What does this mean for you? If you happen to have this particular SNP, which many people do, your body may have an impaired ability to metabolize folic acid from foods and supplements. However, if you take a supplement with the end metabolite of methylfolate, your body will be getting the micronutrient it needs in adequate quantities for your long term health.
Other SNPs that affect the body’s ability to absorb specific nutrients include:
- Vitamin A (a combination of 25 SNPs affects the ability to absorb vitamin A, with the specific effect depending on the specific combination present in a given individual);
- Vitamin D;[14, 15]
- Iron; and
- LDL cholesterol (SNP rs20455, associated with high levels of LDL cholesterol, common in Filipino-American women)
Unique SNP Profiles
Because SNPs are unique to each individual and can have a dramatic impact on health in aggregate, the future of preventive medicine includes everyone understanding his or her unique SNP profile. With such information, not only can the likelihood of acquiring various diseases be estimated, but a doctor can recommend supplements and lifestyle choices that can help compensate for SNPs that prevent normal absorption of certain nutrients. For example, if someone knows that he or she has the the C677T polymorphism, they can take a high-quality methylfolate supplement to reduce the risk of complications that could arise. Companies such as Helix and 23andme are able to map an individual’s SNPs and provide a unique SNP profile. These profiles may be helpful in estimating the risks of acquiring various diseases like celiac, Alzheimer’s, and cancer, indicate food intolerances, recommend dietary changes and useful supplements, and offer additional useful health information.
The scientific research on this is in many ways just getting started and we are a ways away from being able to give everyone an accurate map of not just their genetics, but also methylation profile, interpret it correctly, and give personalized and specific recommendations to address all individual aberrations. Despite this, already there is definite value in getting familiar with this aspect of your physiology and there are some things we do know that could prove helpful for maximizing health potential long term. The testing and especially interpretation of SNPs is an active area of research with exciting potential.