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High False-Positive Rate Found in Consumer Genetic Tests

DNA analysis graphic

(Gerd Altmann, Pixabay)

23 March 2018. Follow-up reviews of results from direct-to-consumer genetic tests show 40 percent of the actionable gene variations reported in the tests, including some indicating disease risk, were erroneous. The study, conducted by Ambry Genetics Corp., a company in the business of lab-based genetic testing, is described in yesterday’s issue of the journal Genetics in Medicine.

Genetic tests marketed directly to the consumer are becoming increasingly popular and economical. While many of these tests analyze a person’s genetic ancestry, some tests are offered to highlight the presence of genetic variations indicating predisposition to a particular disease. The company 23andMe, for example, markets a genetic test that indicates the presence of genes indicating a higher risk for Parkinson’s disease, late-onset Alzheimer’s disease, and several others. In April 2017, FDA authorized 23andMe to provide these tests, and as reported earlier this month in Science & Enterprise, FDA cleared the company to offer tests for certain variations of genes indicating higher risk of some breast and ovarian cancers.

Ambry Genetics, in Aliso Viejo, California, provides laboratory genetic testing for health care providers, with part of its business coming from physicians asking for confirmation of initial genetic tests given by others, including those marketed to consumers. The study, led by Stephany Tandy-Connor, a genetics counseling supervisor at the company, reviewed 49 cases from 2014 to 2016 referred to the company for confirmation by health care providers, and originally tested by direct-to-consumer services. Nearly all (92%) of the cases were women, with the vast majority (74%) not reporting any disease at the time of the test.

The confirmation analyses used high-throughput Sanger sequencing, the so-called gold standard of genetic testing, with the Ambry team comparing the original test results with the follow-up findings. Nearly 9 in 10 (88%) of the genetic variations reported by the initial tests were linked with increased cancer risks. While the follow-up testing confirmed most of the variations in the direct-to-consumer tests, a large proportion — 40 percent — were false positives. In addition, 8 variations of 5 genes classified as higher-risk of cancer and other diseases in the original test, are considered benign by Ambry and other lab-testing services. In some public genetic databases, such as the Exome Sequencing Project and 1000 Genomes, the variations occur at a rate considered too high to be linked to disease.

The authors note that some of the false positives may result from different testing technologies, and the small sample size indicates that larger numbers of direct-to-consumer or DTC test results should be assessed. In a statement issued by Springer, the journal’s publisher, Tandy-Connor says even with the small sample, the results show consumers should get confirmation and professional interpretation, and not rely only on the initial test results. “While DTC results may lead to healthy changes in lifestyle or diet,” she says, “these could also result in unwarranted emotions, including anxiety when someone obtains unexpected information, inaccurate information, or disappointment when receiving a lack of comprehensive diagnostic analysis.”

Tandy-Connor tells more about the study in the following video.

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