It admits its results are "statistical estimates"
January 11, 2020 1:24 PM Subscribe
A host at CBC's Marketplace and her identical twin sent DNA samples to five DNA ancestry companies. The companies all sent back different ancestry results, and two of the companies - 23andme and Living DNA - gave different results for each twin. Article. Video.
That's why Gravel says consumers should take the results generated by these tests with a grain of salt. People need to understand these tests are not subject to the same standard as diagnostic medical testing. They are more like a "recreational scientific activity," he said.
They sucked his brains out!: The real issue is consumer education, to know what you are buying (and, likewise, what you are not buying).
One thing they discuss more in the video than in the article is the tone of advertisements. What they say they're selling in the ads and what they say they're selling in the fine print are two different things.
posted by clawsoon at 2:15 PM on January 11, 2020 [12 favorites]
One thing they discuss more in the video than in the article is the tone of advertisements. What they say they're selling in the ads and what they say they're selling in the fine print are two different things.
posted by clawsoon at 2:15 PM on January 11, 2020 [12 favorites]
I have two thoughts -- send in your spit to the same company several different times to see how varied the results are.
Also, there are police all across this country using genetic information from crime scenes to compare to genetic information on genealogical databases to try to find "relatives" of unidentified suspects in order to track them down.
I had though the whole gene testing thing was more accurate than this, but apparently it's largely guesswork beyond just getting the chain of base pairs. Not quite living as much in the future as I thought.
posted by hippybear at 2:23 PM on January 11, 2020 [1 favorite]
Also, there are police all across this country using genetic information from crime scenes to compare to genetic information on genealogical databases to try to find "relatives" of unidentified suspects in order to track them down.
I had though the whole gene testing thing was more accurate than this, but apparently it's largely guesswork beyond just getting the chain of base pairs. Not quite living as much in the future as I thought.
posted by hippybear at 2:23 PM on January 11, 2020 [1 favorite]
Every time I think about these genetic ancestry tests I think of my friend Peter Cho, who had quite the life changing experience, twice, with what 23andMe was telling him. It's not complete garbage, but it's close, and it is misleading.
Thank you for the detailed technical explanation of what's going on, They sucked his brains out. But you make it sound like it's somehow the consumer's fault that this product that's advertised to tell people their genetic ancestry does not, in fact, tell people their genetic ancestry. There's a lot of problems here but the casual consumer is not the one to blame.
I cancelled my own 23AndMe account recently, on the back of yet more news that your genetic data is not private in an American company's database. If you're curious here's my notes about how to archive and delete your record. Note you can never truly delete your data; copies will continue to exist for at least a decade, out of your control.
Between the threat to privacy, the dubious original value, and the apparent inconsistency of the results I think these home genetics tests should not be sold. SNPs and genetic science are fascinating, but the way it gets packaged into a $100/yr service is terrible.
posted by Nelson at 2:24 PM on January 11, 2020 [19 favorites]
Thank you for the detailed technical explanation of what's going on, They sucked his brains out. But you make it sound like it's somehow the consumer's fault that this product that's advertised to tell people their genetic ancestry does not, in fact, tell people their genetic ancestry. There's a lot of problems here but the casual consumer is not the one to blame.
I cancelled my own 23AndMe account recently, on the back of yet more news that your genetic data is not private in an American company's database. If you're curious here's my notes about how to archive and delete your record. Note you can never truly delete your data; copies will continue to exist for at least a decade, out of your control.
Between the threat to privacy, the dubious original value, and the apparent inconsistency of the results I think these home genetics tests should not be sold. SNPs and genetic science are fascinating, but the way it gets packaged into a $100/yr service is terrible.
posted by Nelson at 2:24 PM on January 11, 2020 [19 favorites]
They sucked his brains out!: Each twin has a unique SNP pattern... So this result is not so surprising, if you know the technical details of what product these companies sell.
If the tiny differences between SNPs in twins leads 23andme to conclude that one twin has ancestors from Ireland and none from England, while the other twin has ancestors from England and none from Ireland, would it be fair to guess that there's some overfitting going on in 23andme's ancestry algorithms?
posted by clawsoon at 2:24 PM on January 11, 2020 [13 favorites]
If the tiny differences between SNPs in twins leads 23andme to conclude that one twin has ancestors from Ireland and none from England, while the other twin has ancestors from England and none from Ireland, would it be fair to guess that there's some overfitting going on in 23andme's ancestry algorithms?
posted by clawsoon at 2:24 PM on January 11, 2020 [13 favorites]
I'm not defending 23andme and how they advertise may certainly be problematic. I'm only writing to say that the result itself about twins is not surprising, based on how the underlying technology works. If anything, I'd agree that these kinds of companies could do more to educate consumers about what they are selling (as well as be more forward about deals leveraged with drug companies to monetize personal genomic data, though that would perhaps be a subject for another post).
posted by They sucked his brains out! at 2:27 PM on January 11, 2020 [4 favorites]
posted by They sucked his brains out! at 2:27 PM on January 11, 2020 [4 favorites]
hippybear: Also, there are police all across this country using genetic information from crime scenes to compare to genetic information on genealogical databases to try to find "relatives" of unidentified suspects in order to track them down.
As I understand it, the ability to connect close relatives using DNA is much, much stronger than the ability to trace ethnic ancestry. With close relatives, it's, "Do 25% or 50% of your SNPs match?", while with ancestry it's more, "Can we pick up a signal 1% or 2% above the background noise?"
posted by clawsoon at 2:30 PM on January 11, 2020 [4 favorites]
As I understand it, the ability to connect close relatives using DNA is much, much stronger than the ability to trace ethnic ancestry. With close relatives, it's, "Do 25% or 50% of your SNPs match?", while with ancestry it's more, "Can we pick up a signal 1% or 2% above the background noise?"
posted by clawsoon at 2:30 PM on January 11, 2020 [4 favorites]
What they say they're selling in the ads and what they say they're selling in the fine print are two different things.
So, business as usual. Always read the fine print. (I don't want to defend these companies but rather to condemn the system.)
posted by hat_eater at 2:53 PM on January 11, 2020 [3 favorites]
So, business as usual. Always read the fine print. (I don't want to defend these companies but rather to condemn the system.)
posted by hat_eater at 2:53 PM on January 11, 2020 [3 favorites]
This question of "picking signal out of noise" and the adjacent problem of over-fitting is really worrying me in several fields all at once.
Here, with 23andMe, it's all the reports issued to consumers who don't understand how uncertain they are. In the adjacent field of archeology there's a lot of amazing data being done correlating a very thin historical DNA record (from fossils) to modern population. The science as summarized in David Reich's book sounds amazing. It also sounds incredibly tenuous, reliant on the most delicate of statistical methods. How many of their results will turn out to be incorrect?
More broadly in the sciences we have replication crisis, often brought about by mis-application of p-testing and other statistical measures that are correct but easy to misuse. And then broadly speaking we've got the entire computer industry in a rush to fit machine learning models to datasets to make predictions like "I recognize that face" or "I know what ad you want to see next" or "this citizen is likely to become a social criminal". Nothing wrong with machine learning per se but it's very, very easy to screw it up and overfit (or underfit) the data and build a bad predictor with errors either gross or subtle.
It feels to me like the science of statistics needs to come up with some simple post-hoc tests that can be applied to the output of subtle statistical work to test it for plausibility. "Do identical twins test for identican genetic ancestry?" is one such test (albeit not statistical). Benford's law is another.
posted by Nelson at 2:53 PM on January 11, 2020 [14 favorites]
Here, with 23andMe, it's all the reports issued to consumers who don't understand how uncertain they are. In the adjacent field of archeology there's a lot of amazing data being done correlating a very thin historical DNA record (from fossils) to modern population. The science as summarized in David Reich's book sounds amazing. It also sounds incredibly tenuous, reliant on the most delicate of statistical methods. How many of their results will turn out to be incorrect?
More broadly in the sciences we have replication crisis, often brought about by mis-application of p-testing and other statistical measures that are correct but easy to misuse. And then broadly speaking we've got the entire computer industry in a rush to fit machine learning models to datasets to make predictions like "I recognize that face" or "I know what ad you want to see next" or "this citizen is likely to become a social criminal". Nothing wrong with machine learning per se but it's very, very easy to screw it up and overfit (or underfit) the data and build a bad predictor with errors either gross or subtle.
It feels to me like the science of statistics needs to come up with some simple post-hoc tests that can be applied to the output of subtle statistical work to test it for plausibility. "Do identical twins test for identican genetic ancestry?" is one such test (albeit not statistical). Benford's law is another.
posted by Nelson at 2:53 PM on January 11, 2020 [14 favorites]
Also, there are police all across this country using genetic information from crime scenes to compare to genetic information on genealogical databases to try to find "relatives" of unidentified suspects in order to track them down.
While its use in criminal cases is concerning, forensic genealogy has proven to be a godsend for cases like this.
posted by Fukiyama at 2:59 PM on January 11, 2020 [1 favorite]
While its use in criminal cases is concerning, forensic genealogy has proven to be a godsend for cases like this.
posted by Fukiyama at 2:59 PM on January 11, 2020 [1 favorite]
The Baroness Von Sketch show looks at DNA kits
posted by nubs at 3:44 PM on January 11, 2020 [8 favorites]
posted by nubs at 3:44 PM on January 11, 2020 [8 favorites]
My friend did 23andMe and found out her dad wasn't her dad, which her mother confirmed (dad is stil in the dark) and that she has a half-sister, whom the database connected her to.
posted by dobbs at 4:00 PM on January 11, 2020 [5 favorites]
posted by dobbs at 4:00 PM on January 11, 2020 [5 favorites]
23andMe displays ancestry results at a default 50% confidence level. If you dial up the confidence numbers, you get more generic results. For me, at the default view, I'm 81% Scandinavian and 12% British/Irish. However, if I set the confidence to 90% the British/Irish component drops by 3/4s and specifically Scandinavian is cut in half. (The results become more "Northern European", "Western European", etc.)
posted by CheeseDigestsAll at 4:51 PM on January 11, 2020 [3 favorites]
posted by CheeseDigestsAll at 4:51 PM on January 11, 2020 [3 favorites]
My brother got a 23andme done and it said he (and hence I) were a pretty boring soup of Gaelic white people from Ireland/Scotland/Wales. Recently, I logged in to find out we'd been updated, with new French lineage! Turns out said French relatives are from Breton... and hence are just additional Gaelic white people. Comrade Doll's was more interesting, with a sizable chunk of Ashkenazi in there lending credence to an old family rumor about how her grandfather might have actually been the town's Jewish doctor, rather than her grandmother's husband. It'd be dramatic to get a notification that she has a cousin... who turns out to be a known descendant of said doctor.
posted by DirtyOldTown at 4:59 PM on January 11, 2020
posted by DirtyOldTown at 4:59 PM on January 11, 2020
Adoptees have found that both 23andMe and Ancestry results are crucial - CRUCIAL - to resolving issues of personal genetic birth identity. As an adoptee, I *implore* you to test at both companies and keep your results public.
Analyses which cast aspersions on consumer genetic testing often both misunderstand and misinterpret the product that these companies are selling and contribute to the erasure of the human rights of many adoptees. Please take this into consideration both before and after you participate in consumer DNA testing. The tests are accurate enough to materially contribute to the resolution of impeded questions of birth identity for many of us.
posted by mwhybark at 6:05 PM on January 11, 2020 [8 favorites]
Analyses which cast aspersions on consumer genetic testing often both misunderstand and misinterpret the product that these companies are selling and contribute to the erasure of the human rights of many adoptees. Please take this into consideration both before and after you participate in consumer DNA testing. The tests are accurate enough to materially contribute to the resolution of impeded questions of birth identity for many of us.
posted by mwhybark at 6:05 PM on January 11, 2020 [8 favorites]
Sorry - it may be tough not to know about your birth parents - but there is no way that I am ever letting any commercial business near my DNA. I do not trust them to do any analysis properly; I do not trust them to use the analysis properly; I do not trust them - full stop.
I don't like having my photo taken; I don't like giving my date of birth; I incinerate all of my personal papers and financial documents; I don't let my passport out of my physical possession. Maybe I am just being paranoic - or maybe it is the result of working with technology for more than 40 years. I cannot conceive of any way that I would voluntarily provide my DNA.
posted by Barbara Spitzer at 6:38 PM on January 11, 2020 [23 favorites]
I don't like having my photo taken; I don't like giving my date of birth; I incinerate all of my personal papers and financial documents; I don't let my passport out of my physical possession. Maybe I am just being paranoic - or maybe it is the result of working with technology for more than 40 years. I cannot conceive of any way that I would voluntarily provide my DNA.
posted by Barbara Spitzer at 6:38 PM on January 11, 2020 [23 favorites]
forensic genealogy has proven to be a godsend for cases like this.
I'm failing to grasp the "godsend" angle there. We're all supposed to submit to a national government database because of one oddball case a decade ago of a person who apparently wanted to remain anonymous?
posted by JackFlash at 6:58 PM on January 11, 2020 [5 favorites]
I'm failing to grasp the "godsend" angle there. We're all supposed to submit to a national government database because of one oddball case a decade ago of a person who apparently wanted to remain anonymous?
posted by JackFlash at 6:58 PM on January 11, 2020 [5 favorites]
As an adoptee, I *implore* you to test at both companies and keep your results public.
Yes, but for someone on the other side of the adoption that may also be a personal catastrophe. You may one day log in and find you have a half brother in your DNA relatives. No explanation or context for that, just surprise! Hope the revelation of a long-held secret doesn't destroy your family!
I personally lived this experience, with one important caveat... I had set my profile to private, so 23AndMe didn't volunteer the unknown half-brother. He found me via other means and then we confirmed the connection via 23AndMe. I'm grateful for that experience and am glad to know him. But if our mother were still alive it would have been much more complicated. Triply so if it had shown up as a surprise one day on a fucking web form.
I think we humans aren't really prepared for impersonal genetic reality vs. family stories. This must be a regular and tragic story with paternity; estimates are 2-15% of people's fathers aren't who they think they are. (Interestingly, the rate varies by culture.) I'm not sure 23AndMe is a good way to learn something as potentially family-wrecking as that your father isn't the man whose genes you inherited.
posted by Nelson at 7:34 PM on January 11, 2020 [8 favorites]
Yes, but for someone on the other side of the adoption that may also be a personal catastrophe. You may one day log in and find you have a half brother in your DNA relatives. No explanation or context for that, just surprise! Hope the revelation of a long-held secret doesn't destroy your family!
I personally lived this experience, with one important caveat... I had set my profile to private, so 23AndMe didn't volunteer the unknown half-brother. He found me via other means and then we confirmed the connection via 23AndMe. I'm grateful for that experience and am glad to know him. But if our mother were still alive it would have been much more complicated. Triply so if it had shown up as a surprise one day on a fucking web form.
I think we humans aren't really prepared for impersonal genetic reality vs. family stories. This must be a regular and tragic story with paternity; estimates are 2-15% of people's fathers aren't who they think they are. (Interestingly, the rate varies by culture.) I'm not sure 23AndMe is a good way to learn something as potentially family-wrecking as that your father isn't the man whose genes you inherited.
posted by Nelson at 7:34 PM on January 11, 2020 [8 favorites]
If the tiny differences between SNPs in twins leads 23andme to conclude that one twin has ancestors from Ireland and none from England, while the other twin has ancestors from England and none from Ireland, would it be fair to guess that there's some overfitting going on in 23andme's ancestry algorithms?
But that's not really what they're saying. The absence of evidence is not evidence of absence: the fact that for one twin, the detected SNPs didn't provide sufficiently robust evidence to resolve English ancestry, while for the other twin they did, doesn't mean 23andMe is saying the first twin doesn't have English ancestry. It just means they couldn't resolve that.
I don't know about other testing agencies, but I've done 23andMe, and they're fairly careful about how they talk about their ancestry results. There's also quite a bit of literature they provide to help you interpret them that I suspect most people skip without reading. I was surprised when I read the article because it opened by making it sound like the two twins tested had completely different results, but when they then presented their testing results, they looked to me to be perfectly compatible. I think a lot of it has to do with the way people interpret terms like "broadly European".
I don't know exactly how 23andMe's algorithms work, of course, but from looking through the information on their site it's pretty clear to me that they don't just look at which SNPs you have to calculate your ancestry: they also look at how those SNPs co-occur in your chromosomes. When people produce sperm and eggs, genetic information from their paired sets of chromosomes are scrambled together. But this doesn't happen with perfectly uniform randomness. Different parts of the chromosome undergo "crossing over" (scrambling) at different rates, and the closer together two SNPs are on a chromosome, the lower the probability that they will be separated from each other from one generation to the next. I don't know but I suspect that 23andMe uses this as an additional source of information to try to assign genetic ancestry to specific geographical regions.
A consequence of this is that you might have two SNPs that individually provide only evidence for "broadly European" ancestry, but if they co-occur on the same genome might provide relatively good evidence for, say, Irish ancestry. Because of the way 23andMe reports its results, this means that the evidence from these SNPs is allocated from the "broadly European" percentage and into the "Irish" percentage. However, this means that estimates for more specific geographical regions are much more sensitive to small differences in the detected SNPs. If either one of these two SNPs is missing in the test results, then the "Irish" evidence provided by both SNPs vanishes. Conversely, the more general "broadly European" category is relatively insensitive to small differences in the detected SNPs, so will easily "soak up" noise in the genetic signal. And in fact if 23andMe looks at co-occurrences not just pairwise but in larger combinations, the sensitivity could be extremely high: intuitively I think it would be on the order of N! but I haven't done the math.
So to me it's not at all surprising that when the two twins have SNP panels that differ by only 0.4%, you can see large differences in the more specific regional assignments. But what you're not seeing is radical differences in the overall regional map, only differences in specificity between the two. Honestly I'm kind of surprised that the computational biologist that CBC spoke to thinks that this is surprising. Maybe my intuitions are radically off, but I don't think so.
posted by biogeo at 9:58 PM on January 11, 2020 [11 favorites]
But that's not really what they're saying. The absence of evidence is not evidence of absence: the fact that for one twin, the detected SNPs didn't provide sufficiently robust evidence to resolve English ancestry, while for the other twin they did, doesn't mean 23andMe is saying the first twin doesn't have English ancestry. It just means they couldn't resolve that.
I don't know about other testing agencies, but I've done 23andMe, and they're fairly careful about how they talk about their ancestry results. There's also quite a bit of literature they provide to help you interpret them that I suspect most people skip without reading. I was surprised when I read the article because it opened by making it sound like the two twins tested had completely different results, but when they then presented their testing results, they looked to me to be perfectly compatible. I think a lot of it has to do with the way people interpret terms like "broadly European".
According to 23andMe's findings, Charlsie has nearly 10 per cent less "broadly European" ancestry than Carly. She also has French and German ancestry (2.6 per cent) that her sister doesn't share.From these sentences, I think people are reading "broadly European" as something other than French and German ancestry. I suppose this is because 23andMe (and other testing agencies, I guess) report ancestry percentages that sum to 100%, giving the impression that if one twin has less "broadly European" and more "French and German" ancestry, they're getting very different results. But that's not really how it works. It's more like nesting boxes. Any genetic markers that are French and German are also "broadly European," but 23andMe resolves them to the most specific region that it can give with some level of statistical confidence. As CheeseDigestsAll says, 23andMe lets you see your results with varying levels of statistical confidence, which is kind of nice. At the 50% level, it may give you quite specific regions for your ancestry results, but all it's saying is that these are more likely than not. If you ask for higher confidence, that specificity is traded for generality, and only markers that are very closely linked with certain ancestral regions will count towards specific areas, with the rest getting lumped into increasingly generic regions like "Western European" or "Broadly European".
I don't know exactly how 23andMe's algorithms work, of course, but from looking through the information on their site it's pretty clear to me that they don't just look at which SNPs you have to calculate your ancestry: they also look at how those SNPs co-occur in your chromosomes. When people produce sperm and eggs, genetic information from their paired sets of chromosomes are scrambled together. But this doesn't happen with perfectly uniform randomness. Different parts of the chromosome undergo "crossing over" (scrambling) at different rates, and the closer together two SNPs are on a chromosome, the lower the probability that they will be separated from each other from one generation to the next. I don't know but I suspect that 23andMe uses this as an additional source of information to try to assign genetic ancestry to specific geographical regions.
A consequence of this is that you might have two SNPs that individually provide only evidence for "broadly European" ancestry, but if they co-occur on the same genome might provide relatively good evidence for, say, Irish ancestry. Because of the way 23andMe reports its results, this means that the evidence from these SNPs is allocated from the "broadly European" percentage and into the "Irish" percentage. However, this means that estimates for more specific geographical regions are much more sensitive to small differences in the detected SNPs. If either one of these two SNPs is missing in the test results, then the "Irish" evidence provided by both SNPs vanishes. Conversely, the more general "broadly European" category is relatively insensitive to small differences in the detected SNPs, so will easily "soak up" noise in the genetic signal. And in fact if 23andMe looks at co-occurrences not just pairwise but in larger combinations, the sensitivity could be extremely high: intuitively I think it would be on the order of N! but I haven't done the math.
So to me it's not at all surprising that when the two twins have SNP panels that differ by only 0.4%, you can see large differences in the more specific regional assignments. But what you're not seeing is radical differences in the overall regional map, only differences in specificity between the two. Honestly I'm kind of surprised that the computational biologist that CBC spoke to thinks that this is surprising. Maybe my intuitions are radically off, but I don't think so.
posted by biogeo at 9:58 PM on January 11, 2020 [11 favorites]
You may one day log in and find you have a half brother in your DNA relatives.
Half-sister, or sister in my preferred usage, but yes, that is the desired outcome. Nelson, we’ve corresponded cordially in the past, I’ll take that up on Sunday, with love and good intent, and with respect to your experience.
posted by mwhybark at 1:19 AM on January 12, 2020 [1 favorite]
Half-sister, or sister in my preferred usage, but yes, that is the desired outcome. Nelson, we’ve corresponded cordially in the past, I’ll take that up on Sunday, with love and good intent, and with respect to your experience.
posted by mwhybark at 1:19 AM on January 12, 2020 [1 favorite]
Do all/any of the companies give you access to their findings at a data level, or just to their conclusions? It seems like it would be more useful to do test-retest or just compare the overall result between companies, to test their accuracy at least.
Then the question of who has the best algorithm is more of business decision?
posted by fizban at 5:41 AM on January 12, 2020
Then the question of who has the best algorithm is more of business decision?
posted by fizban at 5:41 AM on January 12, 2020
The twins are from Sicily. My impression is that Sicily has been conquered or settled by pretty much everybody, from the Greeks and Carthaginians and Romans to the Vandals and Moors and Normans. I can see from that perspective how it would present an interesting genetic ancestry challenge.
posted by clawsoon at 6:31 AM on January 12, 2020
posted by clawsoon at 6:31 AM on January 12, 2020
Do all/any of the companies give you access to their findings at a data level,
23andMe lets you download spreadsheet with a list of chromosome segments and how they're classified at each confidence level.
posted by CheeseDigestsAll at 7:05 AM on January 12, 2020
23andMe lets you download spreadsheet with a list of chromosome segments and how they're classified at each confidence level.
posted by CheeseDigestsAll at 7:05 AM on January 12, 2020
This is relevant to my interests. I got an eighth of Ashkenazi Jewish lineage from my mom and a quarter from my dad, coming to, you know, three-eighths, or 37.5 percent. Ancestry and 23andme have at varying times told me I'm 33 to 41 percent Ashkenazi. It's never been a surprise to me that it's an estimate, but I did have to learn to squint a bit at these numbers. I can, however, understand why plenty of people misinterpret the results, taking them at face value and expressing shock when they're not entirely accurate. Perhaps more warning labels are needed...
The real strength of one's own DNA testing is in genealogy, not ethnic guessing. Sometimes the latter helps (I have a couple drops of blood from Scandinavian ancestors?! Oh, that was from the fun and games in, oh, the sixteenth century among the German bunch) but the distinct value for the individual user is in finding and correlating/confirming family tree matches.
posted by Jubal Kessler at 7:54 AM on January 12, 2020 [1 favorite]
The real strength of one's own DNA testing is in genealogy, not ethnic guessing. Sometimes the latter helps (I have a couple drops of blood from Scandinavian ancestors?! Oh, that was from the fun and games in, oh, the sixteenth century among the German bunch) but the distinct value for the individual user is in finding and correlating/confirming family tree matches.
posted by Jubal Kessler at 7:54 AM on January 12, 2020 [1 favorite]
Jubal Kessler: Perhaps more warning labels are needed...
I wonder if something as simple as percentage ranges would help. Like... why not just tell you "33%-41%", instead of "33%" or "41%"?
posted by clawsoon at 8:35 AM on January 12, 2020
I wonder if something as simple as percentage ranges would help. Like... why not just tell you "33%-41%", instead of "33%" or "41%"?
posted by clawsoon at 8:35 AM on January 12, 2020
I always figured that I would try one of these and get back, like, 50% English, 25% Cocker Spaniel, 12.5% Danish, 12.5% Apple Turnover.
posted by delfin at 9:52 AM on January 12, 2020 [4 favorites]
posted by delfin at 9:52 AM on January 12, 2020 [4 favorites]
I did the test and got back 98.8% chimpanzee!
posted by LizBoBiz at 10:06 AM on January 12, 2020 [2 favorites]
posted by LizBoBiz at 10:06 AM on January 12, 2020 [2 favorites]
hippybear: Also, there are police all across this country using genetic information from crime scenes to compare to genetic information on genealogical databases to try to find "relatives" of unidentified suspects in order to track them down.
As I understand it, the ability to connect close relatives using DNA is much, much stronger than the ability to trace ethnic ancestry. With close relatives, it's, "Do 25% or 50% of your SNPs match?", while with ancestry it's more, "Can we pick up a signal 1% or 2% above the background noise?"
To build on clawsoon's response to hippybear, US police use the CODIS system which looks at short tandem repeats (STRs) not SNPs. This is the same type of test to used for paternity cases, and his handy for building family trees since they STRs follow standard rules of heritability (i.e. every individual will get one copy at random from one parent, and another copy at random from the other) SNPs are heritable, obviously, but they are also more likely to mutate in individuals (a one base pair change is easier to "slip through" DNA replication proofreading). There are commercial DNA tests using STRs instead of SNP-chips, such as Family Tree DNA. Not endorsing them, just mentioning that the market has alternatives I work at an academic molecular biology lab that used to do the lab work for Family Tree years ago but no longer does. I have no pony in this race, but if anyone wants to get a broad genetic profile, I recommend volunteering for Genes For Good. Answer a bunch of health questions, send in your spit, and get like half a million SNPs for your own enjoyment.
posted by lizjohn at 10:15 AM on January 12, 2020 [6 favorites]
As I understand it, the ability to connect close relatives using DNA is much, much stronger than the ability to trace ethnic ancestry. With close relatives, it's, "Do 25% or 50% of your SNPs match?", while with ancestry it's more, "Can we pick up a signal 1% or 2% above the background noise?"
To build on clawsoon's response to hippybear, US police use the CODIS system which looks at short tandem repeats (STRs) not SNPs. This is the same type of test to used for paternity cases, and his handy for building family trees since they STRs follow standard rules of heritability (i.e. every individual will get one copy at random from one parent, and another copy at random from the other) SNPs are heritable, obviously, but they are also more likely to mutate in individuals (a one base pair change is easier to "slip through" DNA replication proofreading). There are commercial DNA tests using STRs instead of SNP-chips, such as Family Tree DNA. Not endorsing them, just mentioning that the market has alternatives I work at an academic molecular biology lab that used to do the lab work for Family Tree years ago but no longer does. I have no pony in this race, but if anyone wants to get a broad genetic profile, I recommend volunteering for Genes For Good. Answer a bunch of health questions, send in your spit, and get like half a million SNPs for your own enjoyment.
posted by lizjohn at 10:15 AM on January 12, 2020 [6 favorites]
DNA Testing and Privacy (Behind the scenes at the 23andMe Lab) - Smarter Every Day 176 is a pretty good bit of interviews and such.
posted by zengargoyle at 12:46 PM on January 12, 2020
posted by zengargoyle at 12:46 PM on January 12, 2020
Turns out, your actual test results from these companies would be more accurately described as 100% marketable.
posted by kafziel at 12:14 AM on January 13, 2020
posted by kafziel at 12:14 AM on January 13, 2020
The fact that 23AndMe used my data to help develop a drug doesn't bother me at all. In fact, that was one of their marketing pitches for why you should sign up. "Get lots of personalized reports. Also, help science by contributing your anonymized data to drug research." They've always been transparent about the fact that was part of their business plan.
What bothered me enough about 23AndMe to delete my account was that a judge decided that a warrant was sufficient to force a company like 23AndMe to share genetic data, even if both they and the genetic donors explicitly don't want to participate in law enforcement searches. 23AndMe isn't the bad guy in this story, they've always tried to keep users' data private from law enforcement, but apparently now they legally can't. Why would I voluntarily join a database that could later help police identify me or some distant relative of mine as involved in a crime? Sure I want to catch the bad guys too, but in no way do I trust American police to do the science correctly nor to be reasonable about what they try to pull a warrant for.
posted by Nelson at 7:38 AM on January 13, 2020 [5 favorites]
What bothered me enough about 23AndMe to delete my account was that a judge decided that a warrant was sufficient to force a company like 23AndMe to share genetic data, even if both they and the genetic donors explicitly don't want to participate in law enforcement searches. 23AndMe isn't the bad guy in this story, they've always tried to keep users' data private from law enforcement, but apparently now they legally can't. Why would I voluntarily join a database that could later help police identify me or some distant relative of mine as involved in a crime? Sure I want to catch the bad guys too, but in no way do I trust American police to do the science correctly nor to be reasonable about what they try to pull a warrant for.
posted by Nelson at 7:38 AM on January 13, 2020 [5 favorites]
The differences in the reports have, I am very confident, nothing to do with spontaneous mutations in early development between the twins. The 0.4% difference in called SNPs is almost certainly due to preparation or contamination of the samples and inherent limitations in the genotyping platform. SNP calls aren't 100%; they are based on the intensity of a reaction of amplified sample DNA with probes on the chip. That intensity can be below the call threshold for some harder to amplify or harder to call SNPs based on haphazard fluctuations. Conversely, in some regions even a tiny amount of DNA (which sticks around for a surprisingly long time) from another individual can amplify enough to set off a probe. If either twin has been pregnant in the past, cells from the fetus (and paternal SNPs) are detectable in blood for years. Sometimes there are technical / manufacturing problems with a given chip as well, leading to wrong calls. Those 0.4% different SNP calls are shifting the "hyper specific European" to "less specific European" especially if the errors place a few SNPs as positive which definitely don't "belong" with the very specific ancestry group.
posted by a robot made out of meat at 9:47 AM on January 13, 2020 [3 favorites]
posted by a robot made out of meat at 9:47 AM on January 13, 2020 [3 favorites]
Yes, but for someone on the other side of the adoption that may also be a personal catastrophe. You may one day log in and find you have a half brother in your DNA relatives. No explanation or context for that, just surprise! Hope the revelation of a long-held secret doesn't destroy your family!
I don't really get this as an argument against DNA testing. It seems to me that it's an argument against cheating on your spouse, and/or keeping long term secrets from them. "I have a child from a previous marriage/relationship" seems like the sort of thing that /should/ come up.
It seems like the sort of thing that happens when someone tells their friend that their significant other is cheating on them, and then they get blamed for ruining the relationship. The friend did not ruin the relationship, the cheating partner did. Likewise: DNA reporting isn't ruining your family. Your family is ruining your family.
posted by Zudz at 10:06 AM on January 13, 2020
I don't really get this as an argument against DNA testing. It seems to me that it's an argument against cheating on your spouse, and/or keeping long term secrets from them. "I have a child from a previous marriage/relationship" seems like the sort of thing that /should/ come up.
It seems like the sort of thing that happens when someone tells their friend that their significant other is cheating on them, and then they get blamed for ruining the relationship. The friend did not ruin the relationship, the cheating partner did. Likewise: DNA reporting isn't ruining your family. Your family is ruining your family.
posted by Zudz at 10:06 AM on January 13, 2020
That's the least empathetic take on it, yes Zudz.
posted by Nelson at 10:23 AM on January 13, 2020 [3 favorites]
posted by Nelson at 10:23 AM on January 13, 2020 [3 favorites]
Also, help science by contributing your anonymized data to drug research
Anonymized data can be used to identify you and family members (cite, cite, cite). Gaps in genomic privacy laws have real consequences.
posted by They sucked his brains out! at 5:24 PM on January 13, 2020 [1 favorite]
Anonymized data can be used to identify you and family members (cite, cite, cite). Gaps in genomic privacy laws have real consequences.
posted by They sucked his brains out! at 5:24 PM on January 13, 2020 [1 favorite]
I know things have come quite a way in the 20+ years since Richard Lewontin's NYRB columns, but the questions he was asking and critiques he offered of genetic testing remain pretty interesting, and quite germane to this conversation.
Does anyone know of a more contemporary evolutionary biologist with that degree of informed macro-level analysis? I feel like everything I've read about 23andMe & co. tends to either be fairly surface-level like the linked piece, or focused on the legal issues rather than the scientific. I have ready access to the purely scientific stuff, but what I'm really looking for is something more like a literature review for the informed layperson.
(Happy to take this to ask if that's more appropriate).
posted by aspersioncast at 11:09 AM on January 14, 2020
Does anyone know of a more contemporary evolutionary biologist with that degree of informed macro-level analysis? I feel like everything I've read about 23andMe & co. tends to either be fairly surface-level like the linked piece, or focused on the legal issues rather than the scientific. I have ready access to the purely scientific stuff, but what I'm really looking for is something more like a literature review for the informed layperson.
(Happy to take this to ask if that's more appropriate).
posted by aspersioncast at 11:09 AM on January 14, 2020
> "I have a child from a previous marriage/relationship" seems like the sort of thing that /should/ come up.
Marriage / relationship / rape / who knows what. There are all kinds of reasons why someone might have had a child, not raised it, and not told future partners.
posted by The corpse in the library at 12:55 PM on January 15, 2020 [1 favorite]
Marriage / relationship / rape / who knows what. There are all kinds of reasons why someone might have had a child, not raised it, and not told future partners.
posted by The corpse in the library at 12:55 PM on January 15, 2020 [1 favorite]
I get what you're saying, mwhybark, but even though I've always wanted to know what my actual background is, I still would never do one of these things. I simply don't trust businesses with information like this. I did do a genetic test when I was diagnosed with cancer two years ago, because my surgeon wanted to know if there was a genetic component to my twin sister's death from ovarian cancer and if so, whether we should look at taking out my ovaries while I was in surgery already. My sister and I were adopted together because it was a private adoption, and back then they would have split us up at an agency, so I have a lot of complicated feelings about this issue.
And in my state, they notify a big research center when you have cancer, and they contact you for participation in a study, which I did, although I was pretty annoyed when I found out they were potentially selling cells to pharmaceutical companies, because I trust them not at all and it infuriates me that they profit off of people that way. So my information is out there, with companies that swear everything I gave them is private, but I have little faith in that when the guvmint comes knocking. Yet I still am not interested in giving my information to a for-profit company that sells these goofy background stories.
Would I like to know what my background really is? Sure. What little I know I can't confirm with anyone; as I understand it my birth mother is deceased and my parents are both gone, and from what little my parents knew about him, bio-dad was a piece of shit, so that's not a relationship I'd ever want even if he was alive. It's just...really complicated, and as much as I would like to know if I really am Welsh and Scandahoovian of some sort, it doesn't sound like they'd be able to tell me in any useful way anything that's really true. I don't know. I just am not sold on letting this stuff out there for anyone to do what they want with it.
posted by kitten kaboodle at 12:31 PM on January 16, 2020 [3 favorites]
And in my state, they notify a big research center when you have cancer, and they contact you for participation in a study, which I did, although I was pretty annoyed when I found out they were potentially selling cells to pharmaceutical companies, because I trust them not at all and it infuriates me that they profit off of people that way. So my information is out there, with companies that swear everything I gave them is private, but I have little faith in that when the guvmint comes knocking. Yet I still am not interested in giving my information to a for-profit company that sells these goofy background stories.
Would I like to know what my background really is? Sure. What little I know I can't confirm with anyone; as I understand it my birth mother is deceased and my parents are both gone, and from what little my parents knew about him, bio-dad was a piece of shit, so that's not a relationship I'd ever want even if he was alive. It's just...really complicated, and as much as I would like to know if I really am Welsh and Scandahoovian of some sort, it doesn't sound like they'd be able to tell me in any useful way anything that's really true. I don't know. I just am not sold on letting this stuff out there for anyone to do what they want with it.
posted by kitten kaboodle at 12:31 PM on January 16, 2020 [3 favorites]
I've been corresponding with Nelson about this and it has helped me to clarify what I am trying to say above.
First, the top-line article, calling into question the scientific accuracy of the genetically-derived ethnicity data that is reported by these sites to the user, is... not wrong, exactly, but misleading. What's particularly at issue with this specific generic style of piece is that it plays toward users' mistaken assumptions about how the consumer sites develop their ethnicity estimates. These estimates change *all the time* as more data is incorporated into the models they use.
Secondly, the tests are not admissible evidence in court for a while bunch of reasons, the most important of which is that in order to reduce the consumer cost, the tests are non-comprehensive and also while presumably conducted under reasonable standards of lab cleanliness, the submitted sample can be problematic due a variety of possible issues, anything from accidental cross-contamination by the submitters, to issues stemming from certain transplants, to lab techs accidentally swapping results.
Nelson's concerns about the use of consumer DNA samples by investigative agencies are worthwhile, I think. The primary popularizer of this use is a person called CeCe Moore, who is a reality-show host and who is the lead mod for a large Facebook group called DNA Detectives, as is her show. By far the majority of the users in the FB group, which has 127319 members, are people attempting to assess the accuracy of the consumer DNA ethnicity estimates, and there are a lot of confused people there. After that group, there is a large contingent of people trying to use consumer DNA data to answer questions regarding their immediate biological families - people like me, as an adoptee, but also people whose parents split up, or whose parent did not disclose their partner, or people whose parent misrepresented their paternity. This last group, people that were conceived via what in the group is known as an NPE, an abbreviation for a sort of clumsy term, "Non-Paternity Event," is larger than any of the other groups, based on the posts I see as they scroll by.
As we move gradually toward a time in which the majority of states in the US have repealed the closed-records status quo for adoptees in closed adoptions, using DNA triangulation to identify one's biological family is an important tool for adoptees who are reluctant to contact their birth families. In many closed-record states, the onus is on the adoptee to initiate the request for contact and the people who hold the power in that relationship are the courts, the involved parties, usually an agency but by no means always, the relinquishing mother, that mother's inheritors of rights should she be unavailable to grant permission, and in some cases the named father on the original birth certificate. This information is not always recorded in the original, and it is not always recorded accurately.
Placing adoptees in the situation of literally having to ask for information which is ours, which fundamentally constitutes who we are, reduces adoptees to second-class citizenship. It does so by permanently consigning us to a juvenile status, one in which we literally have to ask our mother for permission, one in which the court retains custody of our birth identity, one in which we are denied full access to participate in the life of the nation as independent adults. I think donor-conceived people also have a right to full information about the circumstances of their conception, and that access to that information should not be contingent on the donor seeking contact, for essentially the same reasons. Any tool we have that can be used to get around these restrictions is one that I think is important to use.
In the case of people whose paternal and/or maternal origins are simply unknown, due to circumstance or catastrophe, the same potential benefit applies: accessible consumer DNA records provide at least the possibility of identifying one's parents without the requirement of requesting contact.
Requesting contact is hugely fraught. It implies directly the possibility that an adoptee will, in effect, be rejected for a second time by our mothers. We are told all our lives that we have not been rejected by our mothers, that the decision to relinquish was not easy, that it was for the best, and so forth. Some of that is undoubtedly true in many cases, but even if the relinquishment was involuntary or coerced, we still experience it as a rejection. It is different than being orphaned, although one supposes that losing one's mother to suicide could feel quite similar. Thus, many adoptees are fearful of initiating contact, and, when contact is denied, it can be catastrophic emotionally for the adoptee.
Consumer DNA testing with open records access has been extremely useful to me, post-reunion, in that it allowed me to independently confirm each of the facts of my conception and both sides of my natal families. I am engaged in developing my familial relationship with my maternal family and it is going well. I had no idea that my mother and her family would interpret my request for contact as a request to be integrated into the family and I was deeply taken aback by their expectations at first, but determined that approaching this with openness and an assumption of goodwill was the only sensible course of action, and I am glad I did so.
Finally, apologies and thanks to Nelson for indulging my correspondence. I said a whole bunch of this to him in a couple of emails, less concisely, and with many eddies and didoes in my prose. I very much enjoy our conversations and am indebted to him.
posted by mwhybark at 1:32 PM on January 16, 2020 [2 favorites]
First, the top-line article, calling into question the scientific accuracy of the genetically-derived ethnicity data that is reported by these sites to the user, is... not wrong, exactly, but misleading. What's particularly at issue with this specific generic style of piece is that it plays toward users' mistaken assumptions about how the consumer sites develop their ethnicity estimates. These estimates change *all the time* as more data is incorporated into the models they use.
Secondly, the tests are not admissible evidence in court for a while bunch of reasons, the most important of which is that in order to reduce the consumer cost, the tests are non-comprehensive and also while presumably conducted under reasonable standards of lab cleanliness, the submitted sample can be problematic due a variety of possible issues, anything from accidental cross-contamination by the submitters, to issues stemming from certain transplants, to lab techs accidentally swapping results.
Nelson's concerns about the use of consumer DNA samples by investigative agencies are worthwhile, I think. The primary popularizer of this use is a person called CeCe Moore, who is a reality-show host and who is the lead mod for a large Facebook group called DNA Detectives, as is her show. By far the majority of the users in the FB group, which has 127319 members, are people attempting to assess the accuracy of the consumer DNA ethnicity estimates, and there are a lot of confused people there. After that group, there is a large contingent of people trying to use consumer DNA data to answer questions regarding their immediate biological families - people like me, as an adoptee, but also people whose parents split up, or whose parent did not disclose their partner, or people whose parent misrepresented their paternity. This last group, people that were conceived via what in the group is known as an NPE, an abbreviation for a sort of clumsy term, "Non-Paternity Event," is larger than any of the other groups, based on the posts I see as they scroll by.
As we move gradually toward a time in which the majority of states in the US have repealed the closed-records status quo for adoptees in closed adoptions, using DNA triangulation to identify one's biological family is an important tool for adoptees who are reluctant to contact their birth families. In many closed-record states, the onus is on the adoptee to initiate the request for contact and the people who hold the power in that relationship are the courts, the involved parties, usually an agency but by no means always, the relinquishing mother, that mother's inheritors of rights should she be unavailable to grant permission, and in some cases the named father on the original birth certificate. This information is not always recorded in the original, and it is not always recorded accurately.
Placing adoptees in the situation of literally having to ask for information which is ours, which fundamentally constitutes who we are, reduces adoptees to second-class citizenship. It does so by permanently consigning us to a juvenile status, one in which we literally have to ask our mother for permission, one in which the court retains custody of our birth identity, one in which we are denied full access to participate in the life of the nation as independent adults. I think donor-conceived people also have a right to full information about the circumstances of their conception, and that access to that information should not be contingent on the donor seeking contact, for essentially the same reasons. Any tool we have that can be used to get around these restrictions is one that I think is important to use.
In the case of people whose paternal and/or maternal origins are simply unknown, due to circumstance or catastrophe, the same potential benefit applies: accessible consumer DNA records provide at least the possibility of identifying one's parents without the requirement of requesting contact.
Requesting contact is hugely fraught. It implies directly the possibility that an adoptee will, in effect, be rejected for a second time by our mothers. We are told all our lives that we have not been rejected by our mothers, that the decision to relinquish was not easy, that it was for the best, and so forth. Some of that is undoubtedly true in many cases, but even if the relinquishment was involuntary or coerced, we still experience it as a rejection. It is different than being orphaned, although one supposes that losing one's mother to suicide could feel quite similar. Thus, many adoptees are fearful of initiating contact, and, when contact is denied, it can be catastrophic emotionally for the adoptee.
Consumer DNA testing with open records access has been extremely useful to me, post-reunion, in that it allowed me to independently confirm each of the facts of my conception and both sides of my natal families. I am engaged in developing my familial relationship with my maternal family and it is going well. I had no idea that my mother and her family would interpret my request for contact as a request to be integrated into the family and I was deeply taken aback by their expectations at first, but determined that approaching this with openness and an assumption of goodwill was the only sensible course of action, and I am glad I did so.
Finally, apologies and thanks to Nelson for indulging my correspondence. I said a whole bunch of this to him in a couple of emails, less concisely, and with many eddies and didoes in my prose. I very much enjoy our conversations and am indebted to him.
posted by mwhybark at 1:32 PM on January 16, 2020 [2 favorites]
Someone in my FB feed posted this 2018 Atlantic story about DNA testing revealing unexpected parternity results and how Facebook has produced self-organized support groups to help people deal with the fallout.
The story looks at how challenging the discovery can be for the person who has had their identified parentage suddenly change, how threatening and unwelcome the news can be seen as from both sides, and how the group helps their membership overcome these concerns.
(In locating a clean link for this story, I happened to notice that The Atlantic appears to have a long-standing editorial interest in covering the larger story of consumer DNA testing. This was one of at least ten stories covering aspects of this published since 2017.)
posted by mwhybark at 11:49 AM on January 18, 2020 [1 favorite]
The story looks at how challenging the discovery can be for the person who has had their identified parentage suddenly change, how threatening and unwelcome the news can be seen as from both sides, and how the group helps their membership overcome these concerns.
(In locating a clean link for this story, I happened to notice that The Atlantic appears to have a long-standing editorial interest in covering the larger story of consumer DNA testing. This was one of at least ten stories covering aspects of this published since 2017.)
posted by mwhybark at 11:49 AM on January 18, 2020 [1 favorite]
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You send some spit to 23andme, they tell you who you are likely related to and what diseases or other physical attributes you may have, based on patterns of these SNPs.
23andme uses Illumina chips for figuring out what genotypic variants you have in the spit sample you send to them. Illumina is a company that manufactures "chips" that react to the presence or absence of markers in the DNA sample you send to 23andme. Each chip in this platform calls different sets of markers.
These markers often have identifiers associated with them, each called an rsID. They also map variants that do not use rsIDs, and instead use some other internal identifier.
Whatever the identifier, GWAS — Genome-Wide Association Studies — are research projects that analyze populations of people in different ethnicities or other cohorts, looking for over- or under-presence of various markers, compared with the larger human population.
For instance, here is such a GWAS study that is used by 23andme to indicate risk factors for Parkinson's disease, in sample donors who have these variants. There are other such studies for schizophrenia, for autoimmune diseases, and so on.
The power of these studies to make a positive, correct association depends on various factors, but the product 23andme sells is ultimately a packaged summary of a lot of work by researchers around the world.
Getting to the substance of the post, these same markers — SNPs — are used by 23andme to guess at your ancestry. And that's the problem when getting samples from identical twins, because a unique SNP pattern imprints after the fertilized egg splits: So this result is not so surprising, if you know the technical details of what product these companies sell. This is an expected outcome, in fact. The real issue is consumer education, to know what you are buying (and, likewise, what you are not buying).
posted by They sucked his brains out! at 1:55 PM on January 11, 2020 [75 favorites]