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Understanding the Difference Between Genetic Testing Technologies

Danny DeSloover

The technology used in a genetic test makes a big difference in the completeness of the results. There is a common misperception that all genetic tests are created equally and the only difference is what areas they focus on — such as ancestry, digestive flora, prenatal screening, health metrics, or cancer. With all the new options in genetic testing, it’s important to know what type of results you are getting in order to best understand how this information can be used. This article clarifies the differences between two commonly used testing technologies: SNP arrays and Next-Generation Sequencing (NGS).

Array Technology vs Next-Generation Sequencing

The biggest difference between array technologies and NGS is in how, and how much of, the gene is analyzed. Array technologies look at specific parts of a gene at lower resolution. NGS can look at every letter of a gene’s code. This difference means that NGS provides a more complete and thorough analysis than array technologies. Array technology is similar to reading one letter in a paragraph, whereas NGS technology reads every single letter of each word in the paragraph. Because of the level of detail assessed in NGS data, conclusions made are based upon more complete information than for arrays.

In the late 1990’s and early 2000’s, array technology was widely adopted as an effective way to perform population screening for known genetic mutations and variants that are linked to disease. It wasn’t until 2006 that NGS technology became an available option for more efficient DNA analysis. Since then, many labs around the globe have adopted NGS as the core technology for genetic diagnostics. Despite the clear advantages from both a cost and quality perspective, some companies have delayed switching to this improved technology due to some barriers such as the initial equipment cost and required subject matter expertise. Today, NGS is considered the gold-standard for genetic analysis and can now be used cost-effectively.

How Array Technology Works

Array technology looks for specific single-letter changes in the DNA sequence, or single nucleotide polymorphisms (SNPs). If a DNA change is known to be associated with increased risk for a particular disease or trait, also known as a mutation, then this data can be extremely useful in patient care. Let’s take the commonly-known BRCA2 gene as an example. There are more than 1,300 known mutations[2] in the BRCA2 gene. Many of these mutations are associated with an increased risk of several types of cancer in women and men, including breast, ovarian, prostate, pancreatic, and melanoma. Genetic tests that use array technology typically look for only a few mutations within the BRCA2 gene, rather than looking for all 1,300. As a result, arrays produce incomplete information about an individual’s BRCA2 gene sequence.

How Next-Generation Sequencing Technology Works

NGS technology is fundamentally different from array technology in terms of process, output and implications. NGS can look at the entire gene rather than only specific positions. As a result, every letter in the gene can be read in detail and mutations in any part of the gene can be identified.

An Example

One way to illustrate the difference between array technology and NGS technology is through a simple sentence:

The car was red.

A test using array technology may only examine one letter in this sentence. For example, it may look for the “c” in car. If the “c” changed to a “b,” the meaning of the sentence would change:

The bar was red.

While it may be important to know about this change from “c” to “b,” this is not the only possible change in the sentence. For example:

The car was.

In this example, the word “red” is deleted and the sentence no longer makes sense. This change in the sentence would be missed by the test that used array technology to only examine the letter “c,” but would be correctly detected by NGS, which examines the entire sentence from beginning to end.

In the same way, a test that uses array technology to only look for certain mutations in a gene may miss other mutations that can easily be detected by NGS. Stretching this analogy to imagine the human genome as many thousands of sentences that make up an entire book, with each gene being a chapter, the importance of comprehensive testing for mutations in every word of every sentence through NGS technology becomes clear.

How to Find This Information

If you’re interested in getting a genetic test for medical purposes, you can usually look up what technology the lab uses on their website. For example, information about Color’s validation and technology can be found in our white paper where you will see that Color offers a clinical-grade genetic test based on NGS technology. If that information is hard to find online, you can also call the lab directly and ask whether they use array or NGS technology. Alternatively, if you have access to genetic counselors through a physician-ordered test or were referred to a lab for testing, you can ask them what technology the lab uses and how those tests compare to others on the market to help choose which test is right for you.

We hope this information helps you on your path toward understanding your genetics.