Putting Genetic Tests to the Test

Craig Venter and colleagues compare consumer genetic tests and suggest ways to make them more useful.

Geneticist Craig Venter and colleagues have tested two of the leading consumer genomics services and declared the fledgling industry to be promising, but still very early in terms of how useful the information might be.

Credit: Technology Review

Venter, the founder of the J. Craig Venter Institute in San Diego, CA, and collaborators from that institute and from Scripps Translational Science Institute in La Jolla, CA, sent the saliva of five individuals--they don't say whose spit they used--to 23andme and Navigenics, two major online DNA-testing companies both based in the San Francisco Bay area. Venter's team then analyzed and compared the results to see if the sites provided consistent information.

The team compared the five sets of DNA results for the risk of developing 13 diseases, including colon cancer, lupus, type 2 diabetes, and restless leg syndrome.

The results are published today in a commentary in the journal Nature, along with suggestions on how to improve genetic testing as a direct-to-consumer product.

Venter's group found that the raw genetic sequencing data supplied by each company was almost 100 percent consistent. That is, for the 500,000 to 1 million genetic markers tested for each person, the As, Cs, Ts, and Gs were almost exactly the same.

How the genetic testing sites interpreted the data was less consistent. Each used studies in the scientific literature that have scanned human populations for DNA markers associated with risk factors in order to predict whether a person will succumb to a particular disease. A person might have, say, a 30 percent increased risk for type 2 diabetes if they have a particular version of the relevant genetic marker.

For the seven diseases analyzed by the researchers, only about half of the risk factors provided by 23andme and Navigenics agreed for the five patients. For instance, for lupus and type 2 diabetes, three of the five subjects received conflicting results.

Digging deeper, the researchers found that some of the individual risk factors were strikingly different. For psoriasis, 23andme reported a risk factor of 4.02 (four times greater) for one individual, while Navigenics reported only a 1.25 risk factor (25 percent greater), a threefold difference.

In my own experiments, I compared results delivered by several online genetic testing websites: 23andme and Navigenics, and also Iceland-based deCodeme. My results for heart attack produced three different overall heart-attack risks--high from Navigenics, medium from 23andme, and low from deCodeme. I found several less-striking contradictions for diabetes, macular degeneration, and other traits.

Story continues below

The differences arise for two main reasons: because different companies sometimes use different markers, and combinations of markers, to determine an overall risk score for a disease, and because the algorithms the sites use differ in how they weigh the risk factors for different genetic markers.

The Venter study notes that, in some cases, companies define the average population disease risk differently. "Navigenics distinguishes population disease risk between men and women (for example, men are more likely to have heart attacks than women), whereas 23andMe primarily takes into account age (for example, incidence of rheumatoid arthritis increases with age)," the authors write. "This ambiguity in the definition of a 'population' underscores the caution one must exercise when interpreting absolute risk results."