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What are SNPs and Why Are They Important?

What is methylation

Single nucleotide polymorphisms or SNPs (pronounced “snips”) are a common type of genetic variation found among people and are responsible for the diversity among individuals, including whether or not you have curly hair, the interindividual differences in drug response, as well as complex and common diseases. 

Each SNP represents a change in a single DNA building block, called a nucleotide. Four nucleotides exist that occur in various combinations in our DNA to make up genes. If a SNP occurs, it may replace the nucleotide cytosine (C) with the nucleotide thymine (T), for example, in a particular stretch of DNA.

Therefore, a single nucleotide change in a DNA sequence is called as SNP:

Single= One 

Nucleotide= Base+ sugar+ phosphate 

Polymorphism= Alteration

SNPs are found throughout a person’s DNA and occur on average about once in every 1,000 nucleotides which means that each person has roughly 4 to 5 million SNPs in their genome (DNA). These SNPs can be unique or very common and occur in a large percentage of the population. To date, scientists have found more than 100 million SNPs in different populations around the world.

You’re probably wondering why these SNPs are so important. Well, they serve an important role in acting as biological markers to help scientists locate genes that are associated with the disease. When SNPs occur within a gene or in a regulatory region near a gene, they often play a more direct role in the disease by affecting the function of the gene, either causing it to make a protein that works too well, or has less activity than normal, or completely stops its production.

How do SNPs occur?

Basically, SNPs are copying errors.

When a cell is about to divide, it first copies its DNA so that the new cells will each have a complete set of genetic instructions. The cell then divides into two cells with this copied information. Sometimes the cell makes mistakes during the DNA copying process which are like ‘typos’. These typos cause variations in the DNA sequence at certain locations, called single nucleotide polymorphisms.

In some cases, scientists are still trying to determine which SNP is the ancestral (original) version and which are changed versions. SNPs that occur during copying errors are also passed on from one generation to the next and rarely change.  

A SNP is reported in the following way: CYP1A2-rs762551 (A;A), indicating the name of the gene, the rs number (SNP), and what versions you inherited.

SNPs may change the amino acids which are the building blocks for proteins (nonsynonymous) or they can be silent (synonymous), or they can simply occur in the noncoding regions. They may influence gene expression, gene stability, and may therefore contribute to disease development. 

The majority of SNPs have little to no effect on health or development. Some of these SNPs, however, have proven to be very important in the study of human health. 

Why are SNPs important?

Researchers have found SNPs that may help predict an individual’s response to certain drugs, their susceptibility to environmental factors, and their risk of developing particular diseases. SNPs are also used to track the inheritance of disease genes within families such as diabetes, obesity, hypertension, and psychiatric disorders.

Therefore, the identification of these variations in genes and the analysis of their effects leads to a better understanding of their impact on gene function and the health of an individual. This improved knowledge has provided a starting point for the development of SNP markers for medical testing and therefore personalized medication to treat the most common life threatening disorders.

SNP alleles in human disease

Inherited disease susceptibility in humans is most commonly associated with SNPs, and many of these diseases are linked to SNPs involved in how nutrients are metabolized by the body

To put theory into practice, I’ll discuss some examples of how the presence of SNPs can lead to chronic diseases.

Nutrigenomics

Evidence has shown the interaction of genetic background and diet with the development of chronic conditions such as obesity, cardiovascular disease, and cancer that are responsible for the majority of deaths in developed western countries. The nature of these interactions is indeed very complex and therefore does not suggest that the presence of a SNP will cause disease, but that disease development is the result of multiple factors.

Obesity

Obesity is the most common nutrition-related disorder and is the core condition of a group of metabolic abnormalities known as metabolic syndrome which includes insulin resistance, high blood pressure, impaired glucose tolerance, and noninsulin-dependent diabetes mellitus. 

Interestingly, an individual’s susceptibility to becoming obese strongly depends on the genetically determined patterns of energy balance regulation, i.e. are you efficiently metabolizing what you ingest.

Multiple genes encoding core protein and enzymes that regulate energy intake and expenditure have been revealed over the past decade4. It has also been found that food intake control may be affected by SNPs in the genes encoding taste receptors as well as several signaling peptides that are active before and during a meal, such as insulin, leptin, ghrelin, cholecystokinin, and their corresponding receptors.

Cardiovascular disease (CVD)

CVD is the primary diet-related chronic disease of the Western world and can be characterized as a group of multifactorial conditions linked to obesity, atherosclerosis, hypertension, and thrombosis. All of these conditions are known to develop due to both genetic factors and environmental influences, however, diet is considered as one of the main environmental influences and a convincing relationship between diet and CVD risk is well established.

Atherosclerosis (blocked arteries) is the key element in the development and progression of CVD which results from a complex combination of lipid (fat) transport and metabolism disorders together with chronic inflammation. Permanently elevated plasma levels of total cholesterol, LDL cholesterol (bad cholesterol), and triglycerides predispose the individual to the development of atherosclerotic plaques, whereas increased high-density lipoprotein (HDL) cholesterol levels appear to be protective. 

Genetic variation in genes encoding for apolipoproteins, as well as some enzymes and hormones, can alter an individual susceptibility to develop CVD due to their function being compromised. Interestingly, the effects of some of these SNPs can be observed through purposefully changing your diet.

An example of this was seen in a study where individuals with the E4 SNP in the apolipoprotein E gene had significantly higher LDL cholesterol(bad cholesterol) levels after increasing their dietary fat intake in comparison to those with the other (E1, E2, and E3) SNPs receiving equivalent amounts of dietary fat5.

It is, therefore, useful to find out whether you have any of these SNPs to modify your diet accordingly. Food is seen as a major environmental factor in the gene-environment interaction, that if harnessed effectively, can ultimately individualize strategies to improve health, by tailoring the food to individual genotypes.

Dr. Gina Leisching

Dr. Gina Leisching holds a BSc in Functional Human Biology, and Honours degree in Physiological Sciences, as well as a doctorate in human physiology from Stellenbosch University, South Africa. At Gene Food, Dr. Gina uses her expertise to provide evidence-pieces that readers may find helpful and informative.

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