Creating Custom Plans for Every Genetic Variants
What are Genetic Variants and why is it important to your functional health journey?
If I had to pick one discovery in genetic research that has required the biggest reset in how the role of diet and lifestyle is viewed in relationship to overall health, it would have to be this:
Ideal health does not depend on having good genes. It depends on how genes are expressed.
In 1990, when the world took on the Human Genome Project (HGP), it was all about identifying, mapping, and sequencing all the genes in the human genome.
It was discovered that genes only make up 1-2% of human DNA, so the more relevant questions became what regions of human DNA had a function, regardless of whether or not they were a gene, and what role did genetic variations play in gene expression, if any?
The answers to these questions are why genetic research has become so vital to understanding how to achieve the best health outcomes possible. It’s also why I make genetics such a big part of my Nutritional Endocrinology Practitioner Training (NEPT) program.
I see these variants, known as single nucleotide polymorphisms (SNPs), as being the point where genetics and functional healthcare meet.
Understanding SNPs is foundational to effectively using genetics as a functional healthcare tool because it turns out SNPs may have a lot to do with gene expression.
Gene Expression = Protein Synthesis
In my blog post, Why Every Functional Healthcare Practitioner Needs Genetic in Their Practice, I mentioned that genes are all about protein.
A gene is defined as a sequence of DNA that “encodes” information necessary to make a protein. This protein then goes on to perform a function within a cell. How much protein a gene produces, or whether it’s allowed to make any at all is determined by its “gene expression.”(1)
As I mentioned earlier, only 1-2% of the human genome is made up of this “coding” DNA known as genes. The other 98-99% of DNA is located between genes and is called “non-coding” DNA.
The Encyclopedia of DNA Elements (ENCODE)(2) has made it their mission to determine if the non-coding sequences between genes serve a function.
For a non-protein-coding sequence to be considered functional, it would presumably have some effect on how a gene is expressed. In other words, a functional sequence in some way would regulate how much protein is made from a given coded DNA sequence.
Proteins that bind to DNA influence whether a gene is expressed. Chemical modifications of DNA can also prevent or enhance gene expression.
ENCODE used six different approaches to help identify regions of DNA that could be chemically modified or bound by proteins. Each method gave clues as to whether a given sequence influenced gene expression.(3)
In the end, the project identified biochemical activity for 80% of the bases in the genome.
The HGP verified that the human genome is made up of 3 billion base pairs of four related chemicals called nucleic acids or nucleotides. They are adenine, cystine, guanine, and thymine represented by A, C, G, and T in a DNA sequence.
One complete strand of DNA is a sequence of these chemicals, 3 billion letters long.
99.9% of the time, the order of nucleic acids in DNA is exactly the same for everyone. .1% of the time there is a variant in the sequence.
All SNPs are variants, but all variants are not necessarily a SNP. For a variant to qualify as a SNP, it must be found in at least 1% of the population.
The most current numbers show on average, there is approximately one SNP in every 1,000 nucleotides. It is estimated there are about 4 to 5 million SNPs in a person’s genome.(4)
There are two primary ways researchers identify SNPs.
The first method involves large scale projects that require the efforts of multiple institutions, hundreds of scientists, and mega computer power.
Researchers basically compare the genome of thousands of individuals, identifying the differences in their DNA sequences. These differences are sorted, cataloged, and entered into a database that is available to everyone over the internet. If the difference occurs in 1% or more of the population, it is cataloged as a SNP.
The second method that is used has a more tailored approach.
Researchers focus on a particular disease or drug response and select those genes already known to be involved in that specific process. They then compare the DNA sequence of thousands of people known to have that disease or response with thousands that don’t.
In this way scientists can identify SNPs or areas of the genome that correspond to specific diseases or drug reactions.
Where are SNPs found and what do they do?
Most SNPs are found in the DNA between genes and have no effect on health or development. Some, however, are very important to the study of human health and the disease process.
They act as biological markers and help scientists identify or locate genes associated with disease. They help predict an individual’s response to certain drugs and their susceptibility to environmental factors such as toxins and the risk of developing diseases.
SNPs can be used to track the inheritance of disease associated with genetic variants within families.
When they occur within a gene or in a regulatory region near a gene, they may play a more direct role in disease by affecting the gene function.
It’s important to note that SNPs and disease-causing mutations are not the same.
SNPs must show up in 1% of the general population and no known disease causing mutation is that common.
Also, most disease-causing mutations are within a gene’s coding or regulatory region and affect the function of the protein encoded by the gene. SNPs are not necessarily located within genes and don’t always affect the way a protein functions.
SNPs fall into two main categories.(5)
Linked SNPs (Indicative SNPs) do not reside within genes and do not affect protein production or function. However, they do correspond to a particular drug response or to the risk for getting a certain disease.
Causative SNPs affect the way protein functions, correlating with a disease or influencing a person’s response to medication. They come in two forms:
Coding SNPs: located within the coding region of a gene, change the amino acid sequence of genes protein production.
Non-coding SNPs: located within gene’s regulatory sequences and change the timing, location, or level of gene expression. (Changes amount of protein produced.)
DNA testing can have many uses, depending on the focus and reason for the test.
I use DNA testing with clients as a way to shed light on genetic variants that may be at the root of chronic health issues. I also use it as a tool that can provide guidance regarding lifestyle and diet choices that will maximize a client’s chances of achieving their best health. Most DNA tests on the market work for my purposes.
However, what kind of analytic support is offered can make a huge difference in how much information can be gained from looking at a client’s DNA test. Tests may need to be compatible with a secondary program or app that can generate additional reports.
The bottom line is, regardless of how much genetic information is generated, it must be accessible to have any sort of value.
I’ve spent countless hours putting together charts that organize hundreds of the more important SNPs in a way that is more easily read and understood by both practitioners and clients.
Students in my Nutritional Endocrinology Practitioner Training (NEPT) program as well as clients in my Empowered Self-Care Lab have access to my Nutrigenomics program which contains all of these charts.
Understanding the SNPs a client has in their genetic profile is a powerful way to help them understand how diet and lifestyle may be influencing their gene expression and overall health.
If you currently use genetic testing in your practice or are considering adding it to your functional healthcare tool box, be sure the information about SNPs is accessible to both you and your clients.
It will make a huge difference in keeping your practice on the cutting edge of healthcare.