by Sydney Sherman
figures by Aparna Nathan
More likely than not, you or someone you know has taken a genetic test. Whether they are curious about their ethnic roots and family tree or want to determine their risk for developing a certain disease, consumers have access to genetic testing as a simple “spit-and-send” process. We use the technology and rely on the results, but how does a genetic test work? And what can the results tell us?
DNA is the instruction manual for our body to grow and function. Nucleotides are the basic units of DNA; they form the letters that make up the instructions. There are four different nucleotide letters: A, T, C, and G (Figure 1). Our entire genome–a complete set of our DNA–is made of 3 billion pairs of these nucleotides. One nucleotide of each pair is on each strand of the double-stranded DNA molecule. Regions of DNA that give the instructions for how to build proteins are called exons, and regions that dictate when to build each protein (among many other things) are called introns. The DNA in each cell is subdivided into thousands of genes that code for specific traits (hair color, blood type, susceptibility to disease, etc.).
Mutations are DNA nucleotide sequence differences that can be compared between people to identify variations. A mutation in a DNA sequence can result in incorrect building of or amount of proteins, which then leads to improper body functions and disease. Many neurodegenerative diseases are the result of improper protein accumulation. In Alzheimer’s Disease, for example, researchers found that mutations in parts of the DNA result in critical proteins being built improperly.
Not all mutations have a negative effect, however. Some mutations offer advantages: a mutation in gene SLC30A8 has a protective effect, making it 65% less likely that people with risk factors for Type II diabetes actually develop the disease, for instance. Identifying DNA mutations and predicting whether they lead to positive or negative consequences requires knowing the nucleotide arrangement in the region of interest. This can be achieved by DNA sequencing.
How sequencing works
Genetic testing requires determining the exact order of nucleotides (A, T, C, and G) in a DNA strand–a process called sequencing. Sequencing uses DNA extracted from the user’s blood or saliva cells. This DNA serves as a template to build thousands of fragments identical to the template DNA with lengths varying from 1 nucleotide to the total length of the DNA region of interest. Those fragments are sorted by size so the last nucleotide of each fragment can be read in size order from longest to shortest and the total DNA sequence can be determined. This basic process, shown in Figure 2, is used in current sequencing methods.
Not all tests are created equal
The goal of genetic testing is to identify if a person has a mutation linked to a specific disease. For some conditions, there is a known gene mutation that can be identified to diagnose the disease (e.g. Huntington’s disease results from a mutation of the HTT gene). There are several methods of genetic testing currently available. The three most common methods are single nucleotide polymorphism (SNP) genotyping, whole exome sequencing (WES), and whole genome sequencing (WGS). These range in cost, accessibility, and amount of information obtained.
SNP (pronounced “snip”) genotyping is often used to determine if a person carries a genetic predisposition for disorders with well-understood mutations, including breast cancer and celiac disease. SNP genotyping tests a set of specific gene locations to determine which SNP variants are present. At a particular site of a single nucleotide, we can have one of the four different nucleotides (A, T, C, G); the difference of one single nucleotide at the same site between different people is called an SNP “variant.” Variants can also be longer in length than one nucleotide. There are specific nucleotide positions within genes in which a changed nucleotide increases your risk of disease. The cost of SNP genotyping can range from approximately $100 – $500 depending on the number of gene locations tested, making it the cheapest of the test options. Direct-to-consumer products from 23andMe and Ancestry use SNP genotyping for their testing method, but it is also used clinically.
WES and WGS methods are appropriate when testing for a broad array of possible diseases. For example, if a patient goes to a physician with rare or unexplained symptoms, WES or WGS may be used to determine what could be causing the symptoms.
WES sequences all exons (a collection of all protein coding regions of your DNA), which comprise about 1% of the entire genome. If a disease is the result of an altered protein, as many are (e.g. Parkinson’s, Alzheimer’s, cystic fibrosis, to name a few), WES can help diagnose the condition. The cost of exome sequencing ranges from $500-$5,000; this wide range is partly due to differences in sequencing coverage, or how many times the DNA sample is sequenced, with higher coverage tests being more accurate.
WGS sequences your entire genome. WGS provides more information compared to SNP genotyping and WES because it includes information from both exons and introns. However, not all of the information is clinically useful yet because so much of the genome has yet to be studied in depth. Further genetics research continues to advance our understanding of certain parts of the genome that have yet to be linked to specific functions, so this test will become increasingly popular in the future. The cost of WGS ranges from $2,000-$20,000 (a much lower price than the cost for the first WGS which came to $2.7 billion). Currently WGS is used more for genetics research than diagnostics, but it is still available to consumers through companies like Dante Labs.
What do test results tell us about disease?
Broadly, genetic testing provides information about two key outcomes : (1) whether you have genetic variants linked to certain conditions, or (2) whether you have a variant of uncertain significance (VUS), meaning you carry a variant that has not been previously linked to a condition.
Genetics tests come with varying accuracy. Studies have cited as much as a 40% false-positive rate in direct-to-consumer tests identifying mutations. Even so, carrying a specific mutation may increase your risk for a disease but does not guarantee you will develop it. In fact, not all of your genes directly affect your health; many other factors affect which genes are expressed. These factors include diet, exercise, environment (pollution, sun exposure, etc.) and other health habits (smoking, etc.).
Conversely, if a genetic test doesn’t identify a variant increasing your risk for a disease, that doesn’t mean you won’t develop it. As Figure 3 shows, relatively few diseases have been linked to genetic variations. Future genetics research is likely to increase the size of the green circle as more links between diseases and genetic variations become clear. If you have a VUS, research supported by the National Cancer Institute recommends that you recheck each VUS with a genomics database every three years to see if more information is available about the variant.
Is genetic testing right for everyone?
We are surrounded by advertising for genetic tests, with companies claiming they can tell you your risk for disease with a saliva sample. To some extent, these claims are true. Genetic testing is able to identify the risk of developing certain diseases based on DNA variants, but the differences in test methods and the complexity of test results means that not every test gives relevant information.
It is important to understand how DNA dictates your wellbeing and the ways you have control over it (diet, exercise, healthy habits, etc.). Genetic testing offers a look into these relationships, but the process is not one-size-fits-all. Understanding the tests available and information gained from each test can help you determine if genetic testing is right for you, whether to use direct-to-consumer or clinical tests, and which test will provide the answers to your questions.
Sydney Sherman is a first-year Ph.D. student in the Harvard-MIT Health Science and Technology Program.
Aparna Nathan is a third-year Ph.D. student in the Bioinformatics and Integrative Genomics Ph.D. program at Harvard University. You can find her on Twitter as @aparnanathan.
For More Information:
- For a video overview on DNA sequencing, check out this TED-Ed video.
- To learn more about how the first human genome was sequenced, check out the Human Genome Project site.
- To learn how Sanger and Next Generation Sequencing methods work, read this Khan Academy article.
- To read more about direct-to-consumer test types, risks, insurance coverage, and privacy issues, see the National Institute of Health Genetics Home Reference.
- The Genome Aggregation Database (gnomAD) is helpful for staying up to date with genetics research. GnomAD can be searched for specific variants and genes to learn if new links between diseases and genetic variations have been identified.