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Consumer Genetic Tests May Have a Lot of False Positives (theverge.com)
A new study, published in the journal Genetics in Medicine, found that consumer genetic tests bring up a lot of false positives. "In this case, 40 percent of the results from the consumer tests were false positives," reports The Verge, noting that the findings "cover a very small sample size and don't show that consumer tests always have a 40 percent false positive rate." From the report: The research was done by scientists at Ambry Genetics, a medical laboratory in California. By looking through their own database, they found that 49 people had been referred to them because of some worrying results from their consumer genetic tests. Still, scientists at Ambry were able to confirm only 60 percent of the results when they compared the raw data from consumer tests with more thorough genetic tests done by themselves and other clinical laboratories. So, 40 percent of variants in a variety of genes reported in DTC raw data were false positives, meaning that they said a genetic variant was there when it wasn't. (Most of these turned out to be variants linked to cancer.) Additionally, the authors write, some variants classified as "increased risk" were not only classified as "benign" by clinical laboratories, but they were actually common variants.
There's a massive incentive to *find something* if you're paying to have a check done... if you get nothing reported then the value of the test seems to be nothing. If you are told to be "at risk" for some condition then you can go to your friends and tell them that you had no idea and that it was so worth it and that now you can take steps... and that perhaps they should get tested too. The best part is that if you're just reported to be "at risk", rather than an actual diagnosis, there's almost no need for accuracy. If you never develop the condition it will be far in the future, and/or you got 'lucky'.
Most "serious" genetic indicators are either quite rare, or their effect has already become apparent to consumer through other means. Common consumer genotyping tests test hundreds of thousands of SNPs. The rate of errors being at least 0.1-0.6% for these methods, there are bound to be hundreds of errors in a typical test result. People are not interested of benign errors, but are very interested on errors which would indicate a health-threatening condition, and this small fraction of test results gets lots of attention. IMHO, there's nothing strange on the fact that large portion of tests leading to a second round are false positives; it's how statistics and bias in such a situation happens to work.
When it comes to whole genome sequencing, both amount of data and error rates can be considerably higher; people just have to get used to the fact noise in big datasets causes strange effects...
I remember an example from a book on probability: You have a test with a 1% false positive rate and a 1% false negative rate. It tests for a condition present in 1% of the population. 10000 people take your test. 100 of them actually have the condition, so you get 99 true positives from that; the 9900 people without the condition produce 99 false positives. By the criteria in the summary, in your population of people who sought further testing, 50% were false positives, but that doesn't make it a bad test.
All these political pundits keep pushing Elizabeth Warren to get a genetic test to "prove" she has Native American ancestry. They reference web-pages by these DNA testing co's in their claims that its possible to test. First, the vendors' own pages often state that the tests are imperfect, and that they often cannot rule out ethnic links. They are better able to say one is "probably" related to a given group, but poor at ruling out a relationship to a group. They look for specific markers or patterns, but currently not the entire genome.
Besides, Elizabeth going through with such tests is feeding the trolls. According her, her relatives told her when she was young that the family has at least one Native American in their background, and there's no reason to question one's older relatives about that. It's rude to the family, in my opinion, to publicly question their word. I hope she doesn't give in to the trolls the way Obama gave into T about the long-form birth certificate.
I see no reason to make a big deal about it. It's just partisan tiddly wings (which both sides do, by the way). Don't even get me started about T's rude "Pocahontas" jokes in front of a Native American event. Very tacky.
Table-ized A.I.