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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'.
They don't have to. The multiple layers of anonymizing means nobody can provide anything useful. Besides which, there's nothing in there the government can use.
Paranoia is a psychiatric disorders, not a political stance.
It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
Understand that the only useful ancestral data are the YDNA and mtdna haplogroups, and that health data is 90% for the researchers.
It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
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...
By looking at people with worrying results, they are strongly filtering for people will results that are already likely to be false positives.
So that '40% false positive' number is nonsense.
It's not shit on this too much. Anyone who's had to work in any science related field, you're as good as your model and training data. To even make ancillary matches that maybe cause a bit of a 'concern' but later turn out to be benign or a false positive, um, sign me the fuck up? Especially if you're not in the health and welfare camp of "You don't know what you don't want to know". Time is on our side in improvement; of course we will, but I hope it's better for my children and not an ultimate target-on-the-back for pre-healthcare screening (which is already really is) and any future healthcare you plan to get. If accuracy is improved for the right reasons, absolutely, but humanity and greed tell me otherwise.
TFA is making it sound like we have world of mega hypochondriacs --- which probably isn't entirely out of the question with today's social media platform of "Oh everybody, on my way to another dicey check-up, fingers crossed " --- but by any measure, if there are genetic health concerns that run in my blood line, why not entertain it, especially if you want to be proactive and curb or neutralize it, if it's in your immediate control to change it? At least you had some concrete information as opposed to none.
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.
Do you sincerely believe these consumer tests have been so thoroughly anonymized that it can't be undone? Or that they're actually doing it at all? I sure don't.
Oh, really? "We've recovered DNA evidence from a crime scene, we need to search your data for matches and relatives". If you don't think governments can and will abuse this, you're missing the point. If your aunt Lulu did this, and the DNA shows a familial match (surely you realise sites like Ancestry.com sure as shit aren't anonymizing your data), then you can be found. Cross reference one or more of these, and you can get lots of stuff. 23AndMe does both health AND ancestry testing.
Once that data is in the hands of a commercial entity, you have no idea what happens to it.
Thirty years ago what you say was true. Twenty years ago it was seen as fairly fringe because nobody believed the rumours of the level of surveillance in the global telecommunications system -- but we've see the change in that. Ten years ago it was starting to sound plausible that the sheer amount of data out there could be violating our privacy.
Now, if you haven't noticed, this is pretty much a certainty -- it's already happening.
At this point, the level of paranoia needed with your personal data, with screening incoming calls from all of the scam artists (the overwhelming majority of calls I get are clearly fraudulent), reading email to be sure it isn't phishing, and not allowing every analytics company to track every piece of data about you ... we've reached the point where what would have been a clinical disorder is the exact amount of paranoia you need to survive in the modern digital world.
Your TV spies on you, your digital assistant spies on you, your phone spies on you, governments freely exchange our information amongst themselves, and every web site you visit has a bunch of third parties whose business model is spying on you.
And all of this information can be secretly demanded, gathered, and misused by governments.
I'm sorry, but paranoia pretty much needs to be a default state. It's why so many people fall for scams -- precisely because what 30 years ago would have been just crazy paranoia, is now the level of vigilance you need to not get ripped off.
From Nigerian scam emails which want you to send all the data someone would need for identify theft (I've gotten several variations on this in the last week), to calls claiming to be able to reduce your credit card bill without not actually knowing who you are (they just claim to be the 'credit card company'), to the Microsoft tech support scams, to spear phishing of executives, to police forces which have cell-phone surveillance, and governments which routinely ignore due process and just hoover up data (Microsoft in Ireland and data privacy laws) ... if some degree of paranoia isn't your baseline state, you're probably fucked.
These days, paranoia better be a political stance. Because it serves a real and urgent purpose un-thinkable 30 years ago.
Hell, I've had to teach my mother in her late 70's to understand and follow a degree of paranoia, and on numerous occasions it has allowed her to say "I'm sorry, but I don't believe you so go away".
How can you possibly have a 4-digit ID and still think as naively as you seem to? That almost defies belief to me.
No.
He is saying of the people that got a positive result, for certain genes, it was in fact a false positive. No information is provided about what percentage of people taking the test got a false negative or true negative. If a test is incredibly accurate at knowing if you are not at risk, that's still a valid test. Especially if it isn't too expensive or invasive to follow up on positive results to see if they were accurate.
You take the test, it says you're okay you go on with life.
You take the test, it says your're not okay, you get a second opinion.
When 50% of your test positives actually have the condition that is a 50% positive predictive value, which is pretty good.
eventually these tests will be ordered by doctors. And insurance companies have a nasty habit of not paying your doctor if the test comes up clean. After all, if the test was going to come up clean anyway why order it in the first place? It sucks, because it makes doctors hesitant to order tests (since they might not get paid).
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I spent 3 months of vacation in Canada and the USA once. Is that long enough for my DNA to have infused?
But seriously... I've heard that everyone who's an Anglo-Saxon pretty much is up to 10% Scandi (Viking raping and pillaging), 3% 'Jewish' and 2% Neatherthal. Beyond that it's possibly a waste of money.
Not sure why the original article even mentions Family Tree DNA (FTDNA) who do testing only for genealogical purposes. Their name appears only in the Introduction. None of their tests is recommended or (I believe) can be used for medical or health-related purposes. On the other hand, 23AndMe is a big DTC marketer of medical DNA testing and I would bet that most of the tests evaluated in this article were by 23AndMe.
Disclaimer - I have been testing my own and the DNA of others since 2007 with Family Tree DNA, and have no connection with the company other than as a satisfied customer and a volunteer administrator for three genealogical surname DNA projects (Foad, Huntsman, and Mugford).
Do you **REALLY** think these companies are going to put up a legal fight for you when your DNA is requested by the government?
A.C.#2
They don't have to. The multiple layers of anonymizing means nobody can provide anything useful. Besides which, there's nothing in there the government can use. Paranoia is a psychiatric disorders, not a political stance.
If you cared to Google it, you would find that, with a search warrant, law enforcement can obtain genetic information and material from places like 23andMe and Ancestry. In fact, the link below confirms they already have at least once. You can use a pseudonym. Maybe it and the corporate anonymity maze will be enough to slip through the sophisticated clutches of the Law's big data algorithms. GLWT.
https://www.ajc.com/news/national/can-police-legally-obtain-your-dna-from-23andme-ancestry/8eZ24WN7VisoQiHAFbcmjP/
BTW, Paranoia is a political stance. It's so obvious, you don't really need a link, but even so:
https://www.spectator.co.uk/20...
https://en.wikipedia.org/wiki/...
http://www.bbc.com/news/magazine-35382599
I wish I could give you mod points, but I've already commented on this thread... you are exactly right though... without knowing how many tests were performed you know nothing, and can't make a judgement about sensitivity and specificity.
Which has more power: the hammer, or the anvil?
Three years ago, I had my DNA analyzed by 23andme. According to my raw SNP data, there's no evidence of the genes for delayed sleep phase disorder... but I unquestionably have it, and have since childhood (& probably before). I found seemingly blatant discrepancies in a few other reported SNPs that appear to diverge quite a bit from observed reality.
I can think of a few possibilities:
* Promethase incorrectly interpreted my raw data & reported SNPs with incorrect values.
* The lab didn't actually sequence those specific values... it reported them based on indirect markers elsewhere that didn't necessarily pan out in this case
* The sample was contaminated by the lab (unlikely?)
* The lab's test for the relevant SNP was inaccurate... or at least, a lot less precise than the raw results imply.
I'd like to eventually get my genome analyzed again... by a company that uses a different lab, with slightly different test... but reports the results in a form that can be directly compared (SNP-for-SNP) with the original (or at least, deterministically converted into equivalent SNP form) to find discrepancies & get an objective idea about the likely error rate for the first.
Any suggestions for whom to use for round 2?
I depends how the result of the test is used. If it jacks up insurance premiums then 50% false positives could be really bad. If it leads to a lifetime of worry it could be pretty terrible. But if all that happens is someone gets a more expensive, reliable test (cost amoritized over everyone who took the unreliable test) then it's probably not so bad.
const int one = 65536; (Silvermoon, Texture.cs)
SJW, n: "Someone I don't like, and by the way I'm a fuckwit" - AC
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.
DNA can only be used to exonerate, not convict. Law enforcement might use it to identify potential suspects for further scrutiny, but when it comes to a court & jury, the only thing DNA proves is that it either a) could not possibly have been you, or b) might have been someone related to you.
Do you **REALLY** think these companies are going to put up a legal fight for you when your DNA is requested by the government?
Why not send your sample to an overseas lab? Surely somebody here has one to recommend.
My God, it's Full of Source!
OUTSIDE_IP=$(dig +short my.ip @outsideip.net)
At no time did you have to provide your personal data.. You certainly can. But it's not required.
No worries - six cousins have already submitted theirs.
And you bought the access ID with your MasterCard.
My God, it's Full of Source!
OUTSIDE_IP=$(dig +short my.ip @outsideip.net)
The DNA evidence they get constitutes 12 markers that aren't included in ANY of the DNA tests provided off the shelf. It's also so thoroughly discredited, because too few markers are used, that it has virtually no legal value any more.
It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
Yes, I know that's satire, but there are a few things that people might worry about.
Only partially for hair colour. I'm something like 75% brown-haired, 20% red-haired, 5% black-haired. What's law enforcement going to do with that? "Someone who may or may not have hair, which may or may not be absolutely anything at all" is not much of a fit. Epigenetics and diet can alter the ratios. Similar problems exist for eye colour.
Race is falsified by DNA. You carry mutations from just about every human (and several non-human) races.
Height and weight, hmmm, if the diet is good then you can determine both from DNA, which rules out everyone in America and Britain.
Birth date is probably the one trait in the list that could potentially be derived unambiguously from DNA, but it would require a fair amount of DNA and it would require the most expensive tests possible.
It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
Then you've (a) never used a DNA service, (b) never bothered to look up what the police DNA database uses (clue - it's incompatible), (c) don't understand DNA.
You cannot de-anonymize the results, don't give me that crap.
The fact that you can find a criminal pretending to offer a service (and apparently those are the circles you work in) does not make any difference to the status of legitimate services.
DNA cannot be abused.
I probably know more about the last two decades than you do. I certainly know more about what is being done and what can be done.
It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
Do they accept anonymous chunks of gold?
I once bought something even though I wasn't the end user. I once bought something with a prepaid card I paid cash for. I once received a gift.
He's getting rather old, but he's a good mouse.
Many people are buying them as gifts, or are genealogists who buy a lot of them. The fact that your credit card is tied to a DNA sample is no indication that the DNA is yours.
If individual-level genetic data is available (as is the case for at least 23andme), then it can be de-anonymised.
Dr. Erlich also identified a new genetic privacy loophole that allows inferring surname of individuals from simple Internet searches using genetic data.
http://datascience.columbia.ed...
If you have individual level genetic data, fewer than 50 common variants should be enough to uniquely identify a person.
Ask me about repetitive DNA
It isn't. Ignoring the fact that you're a chimera and a mosaic, which means you can have multiple combinations of those, we know from genetic genealogy that 111 markers will be sufficient to uniquely identify the group that comprises every relative up to three steps away (so third cousins, great grandparents, etc).
You'd need far, far more markers to uniquely identify you. And that's useless as your DNA will last up to a million years. Cross-contamination means that unless you can identify how old the DNA is, having the DNA tells you nothing.
(You CAN actually obtain that information, but the standard consumer systems aren't nearly high enough resolution. You'd need full genome sequences from multiple collection spots across the body, plus sequencing of the sample, for that. At roughly $10,000 a pop, plus borrowing a computer powerful enough to determine the point of intercept from the nearest sample, you're looking at more than most police departments have in budget even for coffee and doughnuts. Most crime labs just aren't clean enough or well equipt enough to do such work, they're low-budget hack jobs designed to make a quick buck.)
And then all you'd have is a sample that matches you. Remember, the sample just has an anonymous ID. There's nothing in the testing system's database that links that ID up to your name.
Can the police use it? No, the markers consumer-grade labs collect are not compatible with any police database markers. They look for different things at different points on the genome. Zero overlap and there's nothing they could do to fix it because of the way microarrays work.
It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
Doesn't matter, their samples aren't attached to any personally identifying information, and I can buy a testing kit for anyone. I've bought testing kits for several people. Doesn't mean I'm any of them.
It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
But the authorities have already been using the dna registries in criminal checks. They have done both the "do you have anything on this person". Because they connect up likely family members and unknown brothers automatically I think it's very likely to be a problem. I don't get why you are so hostile about this.
They get a search warrant. Their system shows that there's a few million test tubes storing DNA samples. That's more than the budget for all the police departments in the US.
They obtain the SNP values. Useless, the police database doesn't store SNPs, it stores STRs in one of the less interesting chromosomes. No way to compare the data.
They use an archaeology DNA lab to sequence the crime scene sample because improper storage means it has broken down. It comes up with about a thousand results, because DNA lasts upwards of a million years and there's a lot of cross-contamination. Also, the police will have used improper collection methods. We know from prior cases that police have chased after people who didn't exist because they contaminated their own samples. It happens.
Ok, so they now have samples they can compare, but have blown their entire forensics budget. They compare and find that each of those thousand results maps to a hundred individuals. So they've a hundred thousand suspects. Not helpful.
We know in trials that police don't do this. They're not methodical, they use DNA to try and rig conviction rates. They could use any evidence for that, they just chose something they could spell. Previously, they've used bite marks. The values have no relevance, they use 8 STRs typically. They claim an accuracy of one in ten million (so 700 people on the planet would produce the same results). However, genealogy researchers would put the frequency of 8 STRs at closer to one in ten. The way it is used has no criminological value, it is purely to frighten juries.
It could be used properly in criminology, but that would require no outsourcing, VERY expensive gear, VASTLY improved practices, a LOT of money and a 100% discard of everything obtained so far. Which, in turn, means much higher taxes.
Your average American would prefer fake trials to paying for a decent service.
It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
They get a search warrant. Their system shows that there's a few million test tubes storing DNA samples. That's more than the budget for all the police departments in the US.
The issue addressed wasn't how expensive it is to properly analyze DNA, but whether companies like 23andMe and Ancestry will turn over your DNA to the government. Yes, they will and have.
They obtain the SNP values... They use an archaeology DNA lab to sequence the crime scene sample because improper storage means it has broken down.... DNA lasts upwards of a million years and there's a lot of cross-contamination... They're not methodical, they use DNA to try and rig conviction rates...
Archaeology, archaeogenetics, what do I know? I'm not going to put forensics on trial. PBS's Nova already did that: http://www.pbs.org/wgbh/nova/tech/forensics-on-trial.html
Your average American would prefer fake trials to paying for a decent service.
'Criminal Justice' is a double entendre. For some reason, this brings to mind the Nietzschean allegory about a murder. The sheriff discovered the blacksmith did it. The village had only one blacksmith, though, so they convicted one of the bakers instead.
It isn't. Ignoring the fact that you're a chimera and a mosaic, which means you can have multiple combinations of those, we know from genetic genealogy that 111 markers will be sufficient to uniquely identify the group that comprises every relative up to three steps away (so third cousins, great grandparents, etc).
Fine, if you don't like my 50 common variants number, then I'll suggest 120 variants: 111 [oddly-specific] to get down to familial group, and another 10 or so to identify a single person within that group. Whether it's 50 or 500, that's still well within the realm of cheap targeted SNPchip technology.
You'd need far, far more markers to uniquely identify you.... You'd need full genome sequences from multiple collection spots across the body, plus sequencing of the sample, for that.
There's a big difference between uniquely identifying someone, and fully describing their genome. I agree that a full description of a person's genome would require extensive whole-genome sequencing, but that's not necessary for forensic purposes. For monozygotic twins it gets a bit trickier, but for any other comparisons uniqueness is less than half an hour of nanopore sequencing away:
Rapid re-identification of human samples using portable DNA sequencing
At roughly $10,000 a pop, plus borrowing a computer powerful enough to determine the point of intercept from the nearest sample, you're looking at more than most police departments have in budget even for coffee and doughnuts
Moving away from SNPchips, 40X genome coverage can be done for less than $1000 now.
Estimated PromethION sequencing costs from Clive Brown
Ask me about repetitive DNA