Genetic science 101: terms you’ll encounter with your DNA test results

DNA test results can be confusing if you’re not familiar with biology. The world of genetic science is full of long, boring scientific explanations and acronyms for things we simply cannot pronounce. That’s why we’ve put together an easy-to-read guide to the common terms you’ll encounter in your genetic reports. From SNPs to nutrigenetics, let’s learn about the genes that make us who we are.

What is a gene?

A gene is a segment of the DNA (deoxyribonucleic acid) molecule containing instructions for your body. Genes dictate how, when and where your body makes each of the many thousands of proteins required for life.

We share 99.9% of our genes with other people. It’s that remaining 0.1% of your DNA that makes you who you are. Isn’t that amazing?

DNA testing relies on scientists knowing where to look (within the billions of letters of genetic code) for unique genetic markers that identify the important similarities or differences between us.

What are gene variations?

All of us have a unique genetic makeup. Each gene comprises of various combinations of four “letters” (A, T, C, and G) which make up your genetic code. Your genes combine these “letters” in various ways, spelling out “words”. These “words” specify which amino acids to release, during the production of the proteins required for your body to develop and function.

Gene variations (or polymorphisms) are slight changes in your genetic code. A “single nucleotide polymorphism” (or SNP, pronounced “snip”) occurs when a single genetic letter is changed (one genetic “letter” is be replaced by another).

Gene variations lead to different processes in the body in the same way altering a letter in a word can change its meaning.

One genetic code for a gene may be found more frequently than other genetic codes for that same gene. The genetic codes for genes that appear less frequently are referred to as “variants”. Variations aren’t “good” or “bad”. They’re simply differences in the types of the genes present in our bodies.

The key is knowing which genes you carry, so you make the right exercise, dietary and lifestyle choices to reduce your health risks.

SNPs are part of the reason why we are all different

These SNPs likely occurred a long time ago and have been passed down from generation to generation since.

A SNP in a gene called LCT, for example, is responsible for lactose tolerance. The original polymorphism likely occurred over 10,000 years ago. What probably happened is that this small change occurred in one person, due to a mis-copy of their DNA when their parents reproduced, resulting in a C-to-T change at the base nucleotide level. This person might not have noticed that they could continue to digest lactose as they got older but, as they had children, and passed on the T base nucleotide to various generations, it became more and more common. Eventually, at some point having a T base nucleotide at a certain position in that gene became advantageous; it meant that instead of killing your animals for meat, you could now drink their milk for energy, creating a renewable energy source to get you through tough times.

This is what is known as a “selection pressure”, which led to positive selection of the T nucleotide in certain populations. Today, the vast majority of Northern Europeans have at least one T nucleotide at that particular point in the gene.

Visit our science page to find out which gene variations DNAFit’s DNA test focuses on.

There are two main types of SNPs: synonymous or nonsynonymous

A synonymous SNP does not affect the protein produced by that gene — so we would never know that we have synonymous SNPs unless we had a genetic test done, and it has no effect on us at all.

A nonsynonymous SNP does, however, affect the protein created by the gene. And this is the type of SNP we are interested in — because it helps to explain the differences between us.

There are two types of nonsynonymous SNPs: missense and nonsense

A missense SNP is similar to the types we have discussed already — it causes a change in the amino acid, which changes the protein, which changes the function of that gene. One of the best ways to show this (that I’ve come across) was thought up by Margaret Smith, author of the book “Gene Genius”. Take the sentence below:

The big red cat ate the bat

Note that all those words are three letters long, and each amino acid is three base nucleotides in size. Therefore, we can pretend that each word is an amino acid, and that the sentence is a protein created by our DNA. A missense SNP would result from one letter changing to another, like so:

The big red cat ate the hat.

Here, the b at the start of bat has changed to a h. This creates a different word (amino acid), which creates a different sentence (protein). The sentence still makes sense, however — it just has a slightly different meaning. This is also known as a substitution SNP; and the vast majority of SNPs that are tested for are substitutions.

There is also a type of missense SNP called an insertion/deletion. These are fairly common, and we will meet three examples later, in the genes ACE, GSTM1, and GSTT1. In this case, instead of there being a substitution, something within the DNA is deleted, which again causes a slight change in the sentence. This might look like so:

The big red cat ate the bat

Changing to:

The red cat ate the bat

This is an example of a deletion SNP — the word “big” has been removed. The sentence (protein) still makes sense, however. There is also an insertion, which would look like:

The big red cat ate the bat

Changing to:

The big red cat ate the big bat.

As you can see, both make sense, but the meaning of each is slightly different — as such, insertion/deletion polymorphisms can alter the function of the proteins they create.

The second type of nonsynonymous SNP, a nonsense one, is slightly different. Here, the change of one letter to another makes no sense (as the name suggests), so we go from

The big red cat ate the bat

To

The big red cat fte the bat

As you can see, this sentence no longer makes sense; fte is not a word. When the body comes across something that isn’t a valid combination of letters (word) in our DNA, it stops creating the protein. This means that an unrecognised word acts as a full stop. So, the sentence

The big red cat fte the bat

Becomes:

The big red cat.

It still makes sense, but it has changed the meaning of the sentence, similar to the previous example. When this happens, it’s called a premature stop codon — which is a scientific way of saying the body stops creating the protein at that point. A gene we will meet later on, ACTN3, is an example of a SNP that creates a premature stop codon.

There are some other words we need to understand when discussing genetics. The first of these is allele.

What is an allele?

For each SNP that we test for, there can be two different alleles, taken from the standard base nucleotides A, T, C and G. So, for the LCT gene, the SNP we are interested in can have two alleles, C or T. We get one allele from our father, and one allele from our mother, meaning that we can either have two C alleles, two T alleles, or one C allele and one T allele.

What is your genotype?

The combination of alleles is called the genotype, which is the type of gene you have — so again for the LCT gene there are three different genotypes for that specific SNP; the CC genotype (two C alleles), the TT genotype (two T alleles), and the CT genotype (one C and one T allele). If your two alleles are the same, you are said to be homozygous, homo meaning the same, for that SNP. If you have two different alleles, you are heterozygous, hetero meaning different, for that SNP. So, again with LCT as our example, you can be a CC homozygote, a TT homozygote, or a CT heterozygote.

What are gene mutations?

You might have heard of the word mutation when it comes to genes. In essence, a mutation and a SNP are the same thing — a small change at the DNA level. The difference is how prevalent they are.

Typically, if this genetic change occurs in more than 1% of people, then it’s called a SNP. If it occurs in less than 1% of people, it’s called a mutation. Why is 1% the cut-off point? No-one really knows — it was just arbitrarily decided at some point, and it’s a nice round number, so why not?

What are reference SNP numbers?

Another thing we need to be aware of is something called rs (reference SNP) numbers. Because genes can be very long, they can actually have more than one SNP within them. An example of this is the gene MTHFR, which again we will meet later. There are more than ten known SNPs within this gene. If I’m talking about a SNP with someone else, it’s important to ensure that we are talking about the same one, to avoid confusion.

To do this, SNPs are given a reference SNP ID number, which can be shortened to rs#, said as “rs number”. This is the particular point in the gene that the SNP occurs, which means we can be sure we’re talking about the right one.

Nutrition + Genetics = Nutrigenetics

Nutrigenetics studies how individual genetic variations respond to our diet, exercise and lifestyle. The combination of nature vs. nurture can cause your genes to be “expressed” in a different way. Nutrigenetics helps us identify how to best achieve our own, individual optimal health according to our body’s preferences and requirements.

Personalising your fitness and nutrition according to your genetic profile helps you live a longer, healthier and happier life.

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This article was originally published on the DNAFit Knowledge Hub.