I spent years working for a company which performed genetic testing for a variety of conditions, germline and somatic (IE, cancer).
Internally, the results we accumulated were only used for providing diagnoses, estimating population frequencies, and writing papers.
Other companies, however, like Guardant Health and Foundation One, initially provided inexpensive or free tests in order to build enormous patient data stores and were then bought by large pharmaceutical companies primarily for this data.
In the end, the patients were the product, and the cheap/discounted tests were overhead cost in taking advantage of these people. I do not know where these companies are now, but my distaste for the industry was a large part of why I've chosen a different field of research.
Im curious why do you find that distasteful assuming there was a chain of consent somewhere in there. Data security is super important as are chains of unbroken informed consent, for using someones individual data in a study. But pharmas getting to see patient data is not something I have a problem with. If you want new cures for diseases how could you possibly have an issue with that? There is no law really stopping pharmas directly interacting with health providers, instead they choose these third party intermediaries because everyone has this unrealised "distaste" in their minds. What's distasteful about the institutions that produce cures having a clear view of the disease? Long term genetics is not even private data, once its cheap enough and portable enough there will be companies sequencing all humans from just the environment through metagenomics. What if you have a rare variant and I can see it at the local brothel as well as at a work place and at a home in large copy number. The future is Google/Facebook style of genetics regardless of what you think its going to be like. The sort of super strong blanket regulation required to block that would destroy any positive value of the technology. Your super secret data is only super secret right now because of a limit in technology and scope of the market. In 50 years genetic data will be as valued by people as their home address, especially as high value products become available for presenting companies with their data. I really dont have a problem with this. Smart watches are a larger existential threat to say insurance premiums for all of us.
I understand the motivation to leave a field if the practices are dishonest. I've been there, too.
However, did you note whether or not these efforts may have been positive contributions to the healthcare of humans? I would imagine gathering health data from a large population has the potential to yield remarkable results.
Bingo! You just described 23andme, Anchestry and some others.
Fun fact: you can't make any reasonable profit off of sequencing human DNA at $49 per pop. Its just won't happen. Maybe with technology in iPhone250 in year 3560, but sorry not today.
Back in a day when I was a Noogler, I had interesing conversation on data scraping and purity of infornation in DNA sequencing database. Basically I was explain it will eventually be sold to insurance companies so that they could estimate your premiums better based on probability of your future diseases. As you can imagine that's a gold mine for any large or mid health insurance provider out there. I was also explained how data verofication makes sure of consistency; for example, if male order a kit (via credit card [prepaids dont work bc they cant know your identity]) but result came as female, such result would not be marked as purity and never sold. There are many other checks and balances, but you get the point.
Bottom line: if you want to get the kit and test your DNA out of fun, at least make sure your identity is not obvious.
I've never done one of these genetic tests. Partly because it's scary to me to learn what diseases I'm likely to get as I get older, but also I just don't want that information in some else's database. We're very fearful of what Google and Facebook already knows about us now imagine they buy 23andMe and then join all their data about you with your DNA (which you've already willingly given up and allowed them to "profile".
Google/Facebook user behavioral data + their users' DNA is about as scary invasive as it gets.
On the other side of this, if massive databases of DNA and medical histories were accumulated, it's possible a great amount of human suffering and harm could be solved by aggressively mining this data to find out the connection between DNA and various diseases.
I mean, besides being denied health insurance because of what someone might find in your DNA, why are you so afraid of something even having your DNA, because it might result in GATACA-like society? If so, we need strong legal protections against discrimination by DNA, but we can't throw out the baby with the bathwater.
There's too much good that can be done to human wealth and welfare by eradicating disease and paranoia about theoretical danger should be challenged into laws to protect against discrimination.
What do you think Facebook + DNA is going to do to harm you? Try to sell you a pharmaceutical or medical treatment? A cure for balding or erectile disfunction?
I did 23andMe many years ago around when it first came out (and I therefore have access to certain results others can’t get since this was pre-FDA settlement).
At the time, I ignored the fact that it said I was 4x more likely to develop colon cancer (I was in early 20s). My sister was diagnosed with colon cancer 3 years ago. When you are a woman diagnosed in your early 30s, apparently it is due to genetics. She discovered it by going to three different doctors after insisting she wasn’t feeling well and that it felt “deeply internal”. The doctor who suggested a colonoscopy did so because he had an internship for a year at a cancer clinic in Boston. The others thought it was in her head. Well they found a malicious tumor and the prognosis from the nations leading cancer clinic was to remove her colon, her uterus and ovaries and large intestines (in their entirety). You can imagine this is a lot to ask of anyone. We asked for data that supported the conclusion that if we don’t remove all of these parts the cancer would spread to her ovaries and kill her and there was literally none to be had. It was 100% based on the doctors personal experience (again we were at one of the top clinics in the world for this).
There is something structurally off with the modern medical system. I believe it relies too heavily on anecdotal experience and memory. I don’t know about you but I can’t remember what I ate yesterday. I think services like 23andMe are on to something, if only as a data point to empower patients to self advocate. We did nothing with the data but he moment I got the phone call I couldn’t help but wonder if we could have found this earlier.
I’ve thought since consumer-level genetic testing first came out that there would be a place for a company to do it fully, truly anonymized using tor+crypto or something similar. It’s a bit surprising to me that it doesn’t exist yet; if I had the right background I’d probably go for it myself. There has to be a decent number of people that want to know, but don’t want anyone else to.
I did 23andme back before they had to stop doing some of the medical stuff. They discovered a serious and potentially harmful mutation that I had. I showed my GP who then confirmed it with other tests. It's something that could kill me, and knowing about it allows me to avoid situations where it could.
The ancestry stuff is really really cool too. I'm 2.7% neanderthal! My whole family discovered aspects of our history that we didn't expect.
It really is scary. They claim to anonymise the data, but to me it feels like removing your name and address from your DNA is like removing the make and model from a car schematic (where only one model was produced).
I wanted to know. It turns out I’m a carrier for cystic fibrosis, and my wife is not. If we were both carriers, we might have chosen to adopt children rather than have our own. So there is more to learn than just your future health. It’s also interesting seeing who my distant cousins are.
Of special concern would be entities like FB and LinkedIn having thins kind of data _and_ availing it to private health insurance as well as potential future private sector employers.
Aren't these PCR tests against known sequences of base pairs? It's not like they're sequencing your DNA or anything, they are just testing for the presence of selected markers. I don't think the data they have is meaningful outside the context of the tests.
I feel I'm in an interesting scenario in that both of my parents have done 23andme, but I have all the concerns you have.
You're not just making this choice for yourself, you're making it (to some degree) for everyone you are or will ever be related to. That has profound implications that people aren't entirely considering when they spend the $50 (or whatever) and spit in a cup.
This doesn't test the full gene sequence, only a few SNPs. Say someone does the test, and it comes back positive. They then call all their relatives. Those relatives have the choice of getting the same test done with 23andMe, or seeing their doctor. Usually proper BRCA gene tests are only reimbursed under certain circumstances, so mostly the relative will have to pay at least $500 to get tested properly. Most of them will just go to 23andMe. The growth in testing because of this effect is going to be significant. All the hard work of doing this kind of testing eg counselling, detailed family pedigrees, contacting family members, discussion of pros/cons of testing etc is being put back onto the individual and their healthcare providers. Good for 23andMe I guess, especially since their value seems tied to how much data they have. Whether this is net beneficial to society I'm not so sure.
"23andMe demonstrated a high level of accuracy (greater than 99% concordance to Sanger sequencing) and precision (demonstrated by studies yielding greater than 99% reproducibility and repeatability)"
Sanger sequencing is pretty accurate, on the order of 99.9%. So if 23andMe is matching those at over 99% accuracy and precision, a full sequence may not be necessary. The FDA took a long time to approve this, so I'd imagine it passes their standards as well.
If you are thinking of macro-societal impact... I think you have to ignore the specifics of this particular test and think of the impact of these sorts of test on medicine, culturally.
For example, there's a sort of Principe in medicine that you shouldn't order tests unless you will action treatments based on results. For example, if you detect a risk of breast cancer that can only be avoided by mamosectamy, only do the test if you're willing to to the procedure. Otherwise, all you have is a more stressed out patient. Data gathering is totally different in medicine for such reasons.
The big, relevant exception is cancer, where a statistical, risk estimating approach is commonplace.
In any case, genetic testing (and other ambient data gathering) may give us good reasons to change this approach. It's a transition and taking a step from toy to medicine (this is what 23andme is doing) is en route to such a change. What could emerge downstream is personalized cancer screening protocols. Maybe you should start getting colonoscopies at age 20 and I should start at 60.
Nearby variants are highly correlated due to their spatial proximity, a phenomenon known as linkage disequilibrium. Therefore a dense array of SNP genotypes is often sufficient to make statistically accurate inferences about the portion of the genome you do not directly assay. I myself have used this strategy to estimate my risk for possessing the ApoE variants from my 23andme callset. Is this 100% accurate? Of course not; no medical diagnostic is. But it is accurate enough to be used as a screening procedure in a lot of cases.
I haven't read through the T&Cs at 23andMe, but can this data be cross referred to (bought by) by insurance companies to quote me an insurance price depending on the outcome of 23andMe analysis ?
Or even by mortgage providers for that matter ? Or potential employers ?
They probably will partner up with insurance company’s and will provide discounts if you take this test as part of your physical. And increase it if you don’t or start at a higher price for all products that the client doesn’t take the test. Yeah it’s gonna come to that
> They probably will partner up with insurance company’s and will provide discounts if you take this test as part of your physical. And increase it if you don’t or start at a higher price for all products that the client doesn’t take the test. Yeah it’s gonna come to that
Even if they could do that [0], once you (and presumably they) get the results they can't discriminate based on them due to the Genetic Information Nondiscrimination Act of 2008, so there is very little incentive for them to pressure you to take the test.
[0] They can't, AFAICT, also because of the GNA, though employer-sponsored insurance might be able to back door something similar through a voluntary employer-based wellness program nominally separate from insurance.
Insurance companies already _can_ do this today, but the practice is uncommon or nonexistent. Why do you think that 23andMe being granted FDA authorization would be the final tipping point to begin this behavior?
If the current FCC approved something, I wouldn't assume that it was approved on its merits. Is the FDA better? An honest question; I don't know much about its current performance or composition, but it's under the same political control as the FCC.
Unfortunately, it seems that you're out of luck if you're outside of the US, but you do get the raw data regardless.
Is there a tool which can help analyze this raw data? If not, I think it would be beneficial to create one, but I imagine this might be hard. Does anyone know how difficult it is to programatically test the genome, as 23andMe provides it, for various genetic disease risks? Is research on this easily available? Would a person need a significant know-how in the field, or can this be done by someone after a reasonable amount of reading on the subject?
geneticgenie.org analyzes your 23andme data. You can upload raw data or just link your 23andme with oauth. It might be more narrow in scope than what you had in mind since it is primarily used to generate a methylation and detox profile. I used it primarily to determine if I had a MTFHR mutation but it was helpful since it showed other potential issues with my methylation system.
I don't know how hard it would be to programmatically do, but if geneticgenie is any proof, it can be done.
I wonder how this stacks up vs other BRCA tests in terms of performance and coverage of common variants. And also whether it is cheaper to use their DTC test rather than going to a doctor and getting insurance to cover the test? I assume this is not a sequencing based test?
It's a SNP chip and only covers a few common mutations.
To anyone who wants to know for sure whether you're at increased risk of breast cancer, you'll want to get a test that sequences all the known mutations, along with another half-dozen or so genes that can have essentially the same effect as a damaging mutation in BRCA. I'd also urge you to find a genetic counselor, who can help explain the diagnosis in detail, as well as the limitations of the each kind of test.
What I did a while back is download the raw data and run it through https://promethease.com/. Will tell you a lot more about risks, drug interactions. What it does is it compares your data to that of all the journal papers and research around that gene. Interestingly I have a SNP that is correlated with lack of empathy and another one that is the "warrior" gene. The BRCA SNPs would be identified.
Hmm. How long before health insurers use this to, uh, "personalize" rates? Note that many have wellness programs that incent employees to present blood samples.
[+] [-] stochastic_monk|8 years ago|reply
Internally, the results we accumulated were only used for providing diagnoses, estimating population frequencies, and writing papers.
Other companies, however, like Guardant Health and Foundation One, initially provided inexpensive or free tests in order to build enormous patient data stores and were then bought by large pharmaceutical companies primarily for this data.
In the end, the patients were the product, and the cheap/discounted tests were overhead cost in taking advantage of these people. I do not know where these companies are now, but my distaste for the industry was a large part of why I've chosen a different field of research.
[+] [-] Ultimatt|8 years ago|reply
[+] [-] ra1n85|8 years ago|reply
However, did you note whether or not these efforts may have been positive contributions to the healthcare of humans? I would imagine gathering health data from a large population has the potential to yield remarkable results.
[+] [-] Symmetry|8 years ago|reply
[+] [-] golergka|8 years ago|reply
[+] [-] joering2|8 years ago|reply
Fun fact: you can't make any reasonable profit off of sequencing human DNA at $49 per pop. Its just won't happen. Maybe with technology in iPhone250 in year 3560, but sorry not today.
Back in a day when I was a Noogler, I had interesing conversation on data scraping and purity of infornation in DNA sequencing database. Basically I was explain it will eventually be sold to insurance companies so that they could estimate your premiums better based on probability of your future diseases. As you can imagine that's a gold mine for any large or mid health insurance provider out there. I was also explained how data verofication makes sure of consistency; for example, if male order a kit (via credit card [prepaids dont work bc they cant know your identity]) but result came as female, such result would not be marked as purity and never sold. There are many other checks and balances, but you get the point.
Bottom line: if you want to get the kit and test your DNA out of fun, at least make sure your identity is not obvious.
[+] [-] benwilber0|8 years ago|reply
Google/Facebook user behavioral data + their users' DNA is about as scary invasive as it gets.
[+] [-] cromwellian|8 years ago|reply
I mean, besides being denied health insurance because of what someone might find in your DNA, why are you so afraid of something even having your DNA, because it might result in GATACA-like society? If so, we need strong legal protections against discrimination by DNA, but we can't throw out the baby with the bathwater.
There's too much good that can be done to human wealth and welfare by eradicating disease and paranoia about theoretical danger should be challenged into laws to protect against discrimination.
What do you think Facebook + DNA is going to do to harm you? Try to sell you a pharmaceutical or medical treatment? A cure for balding or erectile disfunction?
[+] [-] lefstathiou|8 years ago|reply
At the time, I ignored the fact that it said I was 4x more likely to develop colon cancer (I was in early 20s). My sister was diagnosed with colon cancer 3 years ago. When you are a woman diagnosed in your early 30s, apparently it is due to genetics. She discovered it by going to three different doctors after insisting she wasn’t feeling well and that it felt “deeply internal”. The doctor who suggested a colonoscopy did so because he had an internship for a year at a cancer clinic in Boston. The others thought it was in her head. Well they found a malicious tumor and the prognosis from the nations leading cancer clinic was to remove her colon, her uterus and ovaries and large intestines (in their entirety). You can imagine this is a lot to ask of anyone. We asked for data that supported the conclusion that if we don’t remove all of these parts the cancer would spread to her ovaries and kill her and there was literally none to be had. It was 100% based on the doctors personal experience (again we were at one of the top clinics in the world for this).
There is something structurally off with the modern medical system. I believe it relies too heavily on anecdotal experience and memory. I don’t know about you but I can’t remember what I ate yesterday. I think services like 23andMe are on to something, if only as a data point to empower patients to self advocate. We did nothing with the data but he moment I got the phone call I couldn’t help but wonder if we could have found this earlier.
[+] [-] merralea|8 years ago|reply
[+] [-] gnarbarian|8 years ago|reply
The ancestry stuff is really really cool too. I'm 2.7% neanderthal! My whole family discovered aspects of our history that we didn't expect.
[+] [-] alex-|8 years ago|reply
[+] [-] seibelj|8 years ago|reply
[+] [-] mc32|8 years ago|reply
[+] [-] Kelbit|8 years ago|reply
[+] [-] nickysielicki|8 years ago|reply
You're not just making this choice for yourself, you're making it (to some degree) for everyone you are or will ever be related to. That has profound implications that people aren't entirely considering when they spend the $50 (or whatever) and spit in a cup.
[+] [-] bpevsner|8 years ago|reply
[+] [-] Gatsky|8 years ago|reply
This doesn't test the full gene sequence, only a few SNPs. Say someone does the test, and it comes back positive. They then call all their relatives. Those relatives have the choice of getting the same test done with 23andMe, or seeing their doctor. Usually proper BRCA gene tests are only reimbursed under certain circumstances, so mostly the relative will have to pay at least $500 to get tested properly. Most of them will just go to 23andMe. The growth in testing because of this effect is going to be significant. All the hard work of doing this kind of testing eg counselling, detailed family pedigrees, contacting family members, discussion of pros/cons of testing etc is being put back onto the individual and their healthcare providers. Good for 23andMe I guess, especially since their value seems tied to how much data they have. Whether this is net beneficial to society I'm not so sure.
[+] [-] ac29|8 years ago|reply
Sanger sequencing is pretty accurate, on the order of 99.9%. So if 23andMe is matching those at over 99% accuracy and precision, a full sequence may not be necessary. The FDA took a long time to approve this, so I'd imagine it passes their standards as well.
[+] [-] dalbasal|8 years ago|reply
For example, there's a sort of Principe in medicine that you shouldn't order tests unless you will action treatments based on results. For example, if you detect a risk of breast cancer that can only be avoided by mamosectamy, only do the test if you're willing to to the procedure. Otherwise, all you have is a more stressed out patient. Data gathering is totally different in medicine for such reasons.
The big, relevant exception is cancer, where a statistical, risk estimating approach is commonplace.
In any case, genetic testing (and other ambient data gathering) may give us good reasons to change this approach. It's a transition and taking a step from toy to medicine (this is what 23andme is doing) is en route to such a change. What could emerge downstream is personalized cancer screening protocols. Maybe you should start getting colonoscopies at age 20 and I should start at 60.
[+] [-] hyperbovine|8 years ago|reply
[+] [-] a13n|8 years ago|reply
https://www.helix.com
(I have no affiliation)
[+] [-] xiphias|8 years ago|reply
[deleted]
[+] [-] stillworks|8 years ago|reply
Or even by mortgage providers for that matter ? Or potential employers ?
[+] [-] m3kw9|8 years ago|reply
[+] [-] dragonwriter|8 years ago|reply
Even if they could do that [0], once you (and presumably they) get the results they can't discriminate based on them due to the Genetic Information Nondiscrimination Act of 2008, so there is very little incentive for them to pressure you to take the test.
[0] They can't, AFAICT, also because of the GNA, though employer-sponsored insurance might be able to back door something similar through a voluntary employer-based wellness program nominally separate from insurance.
[+] [-] coryfklein|8 years ago|reply
[+] [-] forapurpose|8 years ago|reply
[+] [-] BurningFrog|8 years ago|reply
What changed?
[+] [-] randomname2|8 years ago|reply
[+] [-] thegeomaster|8 years ago|reply
Is there a tool which can help analyze this raw data? If not, I think it would be beneficial to create one, but I imagine this might be hard. Does anyone know how difficult it is to programatically test the genome, as 23andMe provides it, for various genetic disease risks? Is research on this easily available? Would a person need a significant know-how in the field, or can this be done by someone after a reasonable amount of reading on the subject?
[+] [-] jgrowl|8 years ago|reply
I don't know how hard it would be to programmatically do, but if geneticgenie is any proof, it can be done.
[+] [-] GordonS|8 years ago|reply
[+] [-] Symmetry|8 years ago|reply
https://www.snpedia.com/index.php/Promethease
[+] [-] retox|8 years ago|reply
http://www.cracked.com/personal-experiences-2522-inside-shad...
[+] [-] aaavl2821|8 years ago|reply
[+] [-] chrisamiller|8 years ago|reply
To anyone who wants to know for sure whether you're at increased risk of breast cancer, you'll want to get a test that sequences all the known mutations, along with another half-dozen or so genes that can have essentially the same effect as a damaging mutation in BRCA. I'd also urge you to find a genetic counselor, who can help explain the diagnosis in detail, as well as the limitations of the each kind of test.
[+] [-] refurb|8 years ago|reply
[+] [-] 2bitencryption|8 years ago|reply
[+] [-] lxchase|8 years ago|reply
[+] [-] calebm|8 years ago|reply
* https://www.snpedia.com/index.php/BRCA1
* https://www.snpedia.com/index.php/BRCA2
Example command to search for a snp: grep rs28897696 genome_your_raw_data.txt
[+] [-] unknown|8 years ago|reply
[deleted]
[+] [-] refurb|8 years ago|reply
[+] [-] tyingq|8 years ago|reply