Popular consumer DNA testing method has a false-positive problem

DNA testing is all the rage these days, but at what cost to your privacy?

Advancements in the world of genetics have opened new doors both for science in general and for everyday people. There are a number of companies focused on consumer DNA testing, whether it’s to screen for potential health problems or to uncover one’s ancestry.

However, new research shows that a popular method could have a major flaw, Gizmodo reports. The method looks at single nucleotide polymorphisms (SNPs), which can be detected with specialized chips. Researchers from the University of Exeter in the U.K. found that this DNA analysis technique creates a high number of false-positive results when screening for rare mutations.

SNP Problems

When the human genome has a malfunction, bad things can happen. Finding where things went wrong is a good way to diagnose certain genetic conditions. However, it also helps predict when a person might be at higher risk of developing a certain condition—such as cancer or heart disease.

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As Gizmodo notes, SNPs are variations of a single nucleotide at some point in a person’s genetic code. To date, more than 300 million SNPs have been discovered. While not all of them cause serious problems, they do serve as good indicators of certain traits.

Understandably, some SNPs are rarer than others—typically the ones associated with more serious health problems.

The research team analyzed data from the U.K. BioBank to draw their conclusions. The study included samples from roughly 50,000 patients who had both SNP testing and a full genome sequence done. This allowed the researchers to analyze the accuracy of the SNP tests, Gizmodo notes.

As mentioned earlier, chips designed to look for SNPs typically do a good job of identifying them. Most chips also look for several SNPs simultaneously to speed up the testing process.

When it comes to common SNPs, there isn’t an issue. The researchers found that the chips are able to identify common SNPs with up to 99 percent accuracy.

The issue occurs when these chips try to spot rare SNPs, those that occur in less than one out of every 100,000 people. In that case, the chips only identified the mutation (or absence of it) correctly 16 percent of the time. They had an astounding false-positive rate of 84 percent, meaning that people are told they have a genetic mutation that isn’t actually there.

Consumer Testing Woes

The biggest issue with this testing flaw is that SNP chips are frequently used by direct-to-consumer DNA testing companies. It is far cheaper and faster than full genomic sequencing. However, it appears that those benefits come at the cost of accuracy.

Study co-author Leigh Jackson said, “We did not look at any particular company, but this will be an issue most companies that offer direct-to-consumer DNA testing will need to consider, as most of them use SNP chip technology.”

Although a full genome sequence can quickly dispel worries about a false-positive, consumers shouldn’t need to worry about whether their results are accurate. It could force someone to go to the doctor and have additional tests that aren’t necessary.

Ultimately, the new research will need to be verified by future studies before further action can be taken. In the meantime, it’s something for consumers to keep in mind before sending a cheek swab for a mail-in DNA test.


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