Accuracy of Genotyping Chips Called into Question

Genotyping chips are used to detect single-nucleotide polymorphisms, the type of DNA used by consumer genetic testing companies to detect variants in a persons genome. These genotyping chips have a false discovery rate of more than 85 percent when screening for rare variants, according to an article from BioRxiv. This finding highlights the danger of direct-to-consumer genetic testing, where customers could “interpret the results at these rare variants literally, without accounting for any possible laboratory errors,” Chiang, a human geneticist at the University of South California Keck School of Medicine, says. “That would be a legitimate concern.”

The chips in which this study came from were supplied by a manufacture named Affymetrix, owned by Thermo Fisher Scientific. They supply their chips to direct-to-consumer companies such as LivingDNA. The companies claim to warn customers not to take their results as a medical diagnosis, but most consumers are not aware of the level of uncertainty in this consumer genetic tests. Other direct-to-consumer companies like 23andMe claim to have a higher accuracy but are still susceptible to false positives in very rare variants.  

An example of a rare variant that may bring about false positives are the BRCA genetic variants. BRCA1 and BRCA2 variants are linked to breast and ovarian cancers, to which there are thousands of known rare variants. The direct-to-consumer companies MyHeritage and 23andMe both announced that they will soon begin providing genetic tests for three variants found on the BRCA1 and BRCA2 genes.

I believe that direct-to-consumer genetic companies are a great way to get the general public interested in genetics and their own genome. It has amazing potential to help people find family and see what part of the world their heritage originates from, but testing for rare genetic variants may still be out of the reach of consumer genetic testing companies. I think that being able to see that if someone has a variant of the BRCA gene would be very helpful in being able to start testing regularly and early to catch any sign of cancer, but with the present rate of false positives in rare variants I believe that we should wait to make this information available to the public until it becomes more accurate.

The Dark Cloud Around Genetic Testing

Thanks to advances in medical science over the years, doctors and patients are now able to rely on genetic tests to determine the occurrence of an array of medical issues. Genetic tests allow doctors to test the likelihood that an unborn child has a medical condition such as Down Syndrome or Edwards syndrome, or if a woman has a high risk for developing breast cancer. However, according to the New England Center for Investigative Reporting (NECIR), many of these genetic tests run a high percentage of false positives.

In the USA alone, there are over 13,000 genetic tests available. However, none of these genetic tests are required to prove to the FDA that the tests are accurate. For example, in a 2014 study by the New England Journal of Medicine, one prenatal genetic test on the market for Edwards syndrome, was found to be accurate only 40% of the time!

Inaccurate results can not only cause extreme emotional trauma, but can also lead to improper diagnoses and unnecessary treatments. In regards to prenatal testing, a patient who learns that their unborn child might have Edwards syndrome or Down syndrome may choose to end the pregnancy. According to a NECIR investigation, every false positive was found to, on average, cost the patient $775,278 worth of unnecessary treatment.

It is important to note that most of these genetic tests are done under the advisory of a genetic counselor, who is a trained medical professional that helps families select the right tests and decide on what to do with those test results. However, according to the NECIR, this is where another problem has recently begun to develop. Unlike with other healthcare professionals, companies are not required by federal law to report payments to genetic counselors. As a result, there is no real way of knowing if a particular genetic counselor has a conflict of interest with a certain test/company.

The way I see it, the FDA really needs to step in, and regulators must crack down on both genetic testing companies and genetic counselors. There should be mandatory guidelines and quality control tests that these genetic tests need to pass to be used, as well as including genetic counselors on the list of healthcare professionals that companies must report payments to. By doing the above, genetic tests will become more accurate, lead to more productive and true outcomes, and keep the evils of business out of the science. 

http://www.popsci.com/theres-no-guarantee-that-genetic-tests-are-accuratehttp://features.necir.org/genetic-counselors-independence