6 ms·

Putting 500k People's DNA Online

95 points by gwern 9y ago

Real_S 9y ago
This article fails to mention any privacy risks to the volunteers. GWAS have proven to be, at best, of little value. In fact, due to the unfortunate way that many researchers chase p-values, these analyses often result in misdirection. What happens? Genome privacy is exchanged for weak science.
- gwern 9y ago
  > This article fails to mention any privacy risks to the volunteers. What privacy risk, exactly? Who has been harmed? 23andMe has been in operation since ~2007 and between them and Ancestry.com and the UKBB and the Japanese BB and others, there must be somewhere on the order of 10 million+ genomes cumulatively. UKBB alone has been the basis for what must be at least hundreds of papers at this point by thousands of researchers or groups. Even further: there are literally thousands of genomes available publicly online from groups like PGP for a decade now, which you can go and download right now, including mine. Is all this not enough? When should we expect to finally see these risks materialize? > GWAS have proven to be, at best, of little value. In fact, due to the unfortunate way that many researchers chase p-values, these analyses often result in misdirection. That is completely wrong. GWASes have an excellent replication record, and were founded on the basis of stringent p-values precisely because of how earlier candidate-gene studies were garbage due to researchers chasing p-values.
  - Real_S 9y ago
    These data can be used to identify their source. This will become easier as more data becomes available. https://news.ycombinator.com/item?id=15209306 https://news.ycombinator.com/item?id=15209306 I guess the value of the data depends on who measures its worth. Replicated p-values lead to multiple publications, which are valuable to academics. But these results can still cause misdirection. What is a low p-value worth if it doesn't lead anywhere?
    - gwern 9y ago
      > These data can be used to identify their source. This will become easier as more data becomes available. Yes, so? (The face paper you link isn't a good example of this anyway, since it's so questionable and re-identification already works much better than that based on stuff like haplotypes.) That's not a real risk, not compared to, you know unlocking the secrets of human genetics. And it has little to do with the research databases: DNA is inherently as far away as it is possible to get from being anonymous, once it started becoming cheap, the loss of genetic privacy was inevitable no matter how it was handled. And it's not that big a deal. We will be much better off for it. > Replicated p-values lead to multiple publications, which are valuable to academics. This is very different from what you were just claiming.
      - rectang 9y ago
        > That's not a real risk, not compared to, you know unlocking the secrets of human genetics. So, it's you who gets to play god and decide to sacrifice individuals for the alleged greater good?
      - Real_S 9y ago
        Unfortunately, GWAS data is unlikely to unlock the secrets of human genetics. We have been in the "post-GWAS era" of genetics for at least a few years now. > And it's not that big a deal. We will be much better off for it. I hope you are right! However, I have doubts. Also, just because sensitive information can be compromised doesn't mean that it should be offered freely.
  - sametmax 9y ago
    It's always important to put this in perspective with the human History. There is no place on earth that lived in peace for ever. Not even for a very long time actually. Any country goes back to times were it's at war on it's own territory, or were it's under a dictatorship. It will be true again for France, the US, Canada, Spain, any country. We will go back there, it's an absolute certainty. Maybe not (hopefully not), in our lifetime. But ignoring this is not only wearing blinders, it's a recipe for making it worse. Things like AI, facebook, the NSA intercepting anything, image recognition, cameras in every streets, tracking devices in every pockets and... DNA databases are going to be weaponized against the population. Even if you don't believe in this (which is always strange to me, but for the sake of the argument, I'll have to acceptit), at least consider that it will make any neutral entity in power more likely to become malevolent by giving it the opportunity to access abusable huge power. Hence, if we want to survive and evolve as a specie, we need to deal with those tools carefully, as they are very potent, and this means what they can do for us is as great as what it can do against us.
    - comboy 9y ago
      This is a super interesting discussion. Both sides make good points. I wonder if in the future cost and technology of sequencing will evolve so much that somebody will start harvesting as much data as possible from places like metro, train stations, malls and so on. This would make it inevitable that your DNA ends up in these databases and you just have to accept it. Just like currently one kind of has to accept that thanks to facial recognition getting even better and cameras everywhere one can be tracked even without any electronic devices.
      - deleted 9y ago
        [deleted]
      - sametmax 9y ago
        You don't have to accept it. You can protest. You can explain. You can vote. You can paie for service respecting you. You can educate. Maybe there are others things to do. There is always a choice. Most people saying there is none are just choosing one cost against another and say it's not a choice. Not blaming, i do the same. But we could avoid the disasters, living by thinking about the society ou simple everyday actions produce. However it's not only very hard to do, but most people are not interested in doing so. Or even to consider the question of society, or how to live ones live. Living on auto pilot is one of humanity's biggest problem. It helped us a lot when we were in survival mode, but now that our own construct is the only real danger to our existence, it really is an hindrance.
  - rectang 9y ago
    > What privacy risk, exactly? People will eventually be identified individually, as inevitably as the people in the AOL search leak years ago. Then they -- and their blood relatives -- will be associated with negative health traits. And then, companies will discriminate -- in hiring, in insurance... anywhere they can. Because it will be financially advantageous to individual companies even though it is detrimental to society as a whole. Because companies are amoral organisms and it is folly to expect them to behave otherwise.
    - jghn 9y ago
      We're probably no more than a year or two away from a sequenced genome being considered PHI for exactly this reason.
  - drewmol 9y ago
    Using the information to assist development of targeted pathogens for biological warfare is an extreme example.
- bpicolo 9y ago
  Not be the case for everybody, but I'm 100% fine with having my genomic data public, especially in the context of research. That's not to say there aren't potential societal contexts where it would be totally awful (e.g. 1930s Germany) but I can't imagine any risk to myself.
  - rectang 9y ago
    Well, I feel sorry for your descendants who won't get hired when it's discovered that they might have inherited BRCA1 and Huntington's Disease from you.
  - patall 9y ago
    But thats not the point. The question is whether you can make data public that, while it belongs to you, also belongs (partially) to other people (your siblings, parents, unborn children ...) who might not want to have their genetic data public. Sure, there is may be no risk to you and a data repository like the one described contains an enourmous value for society in the form of biomedical data but that does not mean you have to give it to everyone without knowing their intention. Especially if they end up knowing something about you that you don't.
    - Real_S 9y ago
      This is an incredibly important point! Openly sharing your genetic information makes both you AND your relatives more vulnerable, with vulnerability decreasing as relatedness decreases. It also reveals potentially sensitive information about family traits.
      - jhbadger 9y ago
        That's one (rather selfish) way of thinking about it. Another way of thinking about it is that you (and everybody else) is better off if more genomic data is available for research. It's worth remembering that genomicists like George Church and Craig Venter have made their genomes publically available for all to access.
    - 9y ago
- patall 9y ago
  > GWAS have proven to be, at best, of little value. In fact, due to the unfortunate way that many researchers chase p-values, these analyses often result in misdirection. I would certainly challenge that, its just that some people considered GWAS as the solution for everything which it clearly isn't, especially because rare mutations where underestimated (and cannot be discriminated in GWAS) and because GWAS was never able to detect the causing variant, just associated/linked genomic loci. And last but not least, the regulatory genome is turning out more and more complex (with interacting variants leading to complexities of O(x^n)) and we do not know yet how it will all be understood, its just that GWAS is one of the better tools we have.
cottonseed 9y ago
I lead the software team in the Neale lab that develops Hail, the software that enabled this analysis: https://hail.is https://hail.is. If you're excited about about applying CS and engineering to enable scientific discovery of massive, fast-growing biological data, get in touch. We just got a bump in funding and we're hiring a number of roles: distributed system database internals, compilers, machine learning, scientific data viz, deployment and operations, and web applications. See our Who's Hiring post: https://news.ycombinator.com/item?id=16288145 https://news.ycombinator.com/item?id=16288145
- dang 9y ago
  This is off topic outside the Who Is Hiring threads. Discussions here are supposed to gratify intellectual curiosity. It sounds like you're in a position to say a lot of interesting things about this topic! but a job ad isn't interesting.
  - cottonseed 9y ago
    Fair, and thanks for clarifying the moderation.
devteambravo 9y ago
That's a terrifying read. See DefCon talk: DEF CON 25 - John Sotos - Genetic Diseases to Guide Digital Hacks of the Human Genome (https://www.youtube.com/watch?v=HKQDSgBHPfY https://www.youtube.com/watch?v=HKQDSgBHPfY)
- John_KZ 9y ago
  That was absolutely horrific. The worst part was this person calling for a "Apollo-level funded" arms race on developing the most horrific bioweapons possible. If you really care about his problem you should call for a ban on related research and keep yourself silent. The further we delay the development of such technology, the better. Some people argue it's inevitable; Well it's not. For almost 100 years, despite their huge potential in war, chemical and biological weapons have seen almost zero development because of the strict enforcement of the Geneva convention. Let's keep it that way.
  - xcvbxzas 9y ago
    I don't think we can confidently say that chemical and biological weapons have seen almost zero development in the last 100 years. We can say as far as we know that's the case, but we also don't have a very compelling reason for knowing. The development of these types of weapons is going to be highly secretive, and not just because of the Geneva convention. Absolutely nothing has gone on in the world in the last 100 years that might tempt the deployment of advanced chemical or biological weapons on any sort of scale. Naturally we haven't seen them used. I also don't see how burying our head in the sand is going to help on this one. At least compared to nuclear weapons, projects on these weapons could be useful for defensive purposes. Everybody is working more or less within the same confines and rules, and I wouldn't be surprised if relatively similar developments were the result. Even if they aren't, the characterization of these weapons can be used to inform and guide the response plans to try to minimize damage in the case of an attack.
    - John_KZ 9y ago
      I have no doubt that biological weapons have been developed to some degree, somewhere, in a well-funded government lab, in complete secrecy. But that is not a problem. This secrecy is what saves us from a race to the bottom. Some government will develop a limited capability of biological warfare. They probably already have. With no information about what their adversaries are doing, they will simply stop. As far as they know, they have developed a state-of-the art biological weapon system, and they are probably correct. One of the reasons that the nuclear arms race happened, was the "openness" of the competition. You can't hide a nuclear explosion. Your adversary knows how sophisticated you are, and they now have to push 1 step further. Biological warfare doesn't have to be like this. Be sure that some Darpa or DoD funded secret project is working on countermeasures, but there's another interesting thing: You can stop biological attacks by quarantine. It's very simple, very effective, and doesn't require developing Armageddon-tier weapons in the process. Another issue that's purposefully isn't discussed in the video is how effective the delivery of these weapons are. Simply put, not very. Viruses, the main attack vector, change in every iteration. There's no guarantee you can infect that many people with an intact version of your weapon. Sooner than later, you genocidal weapon will stop being so selective, because it's evolving for it's own benefit, not yours. And finally, if you really are concerned about this issue, as you should, the right way to fight against it is to find a way to stop the infection and proliferation, to find ways to stop these attacks without accelerating weapons development. There are ways to fight these weapons without building them, and you can definitely do better than starting a public campaign that asks people to develop horrific bioweapons just so we can find a way to stop them later on, maybe.
geobourazanas 9y ago
Hey all, we are a team working toward democratising genetic testing. We are trying to gauge how much people know about genetic testing and what people feel about it. I have a super short form (4 questions only). Would really really appreciate some input from the good folks on this channel! https://joannavass.typeform.com/to/Vy18OL https://joannavass.typeform.com/to/Vy18OL
bob4444 9y ago
I hate to sound like a shill, but this sounds similar to an area Encrypgen (DNA) is trying to reach. (https://encrypgen.com/ https://encrypgen.com/)
lerie82 9y ago
API would be nice

95 points by gwern 9y ago

This article fails to mention any privacy risks to the volunteers. GWAS have proven to be, at best, of little value. In fact, due to the unfortunate way that many researchers chase p-values, these analyses often result in misdirection. What happens? Genome privacy is exchanged for weak science.

gwern 9y ago
> This article fails to mention any privacy risks to the volunteers. What privacy risk, exactly? Who has been harmed? 23andMe has been in operation since ~2007 and between them and Ancestry.com and the UKBB and the Japanese BB and others, there must be somewhere on the order of 10 million+ genomes cumulatively. UKBB alone has been the basis for what must be at least hundreds of papers at this point by thousands of researchers or groups. Even further: there are literally thousands of genomes available publicly online from groups like PGP for a decade now, which you can go and download right now, including mine. Is all this not enough? When should we expect to finally see these risks materialize? > GWAS have proven to be, at best, of little value. In fact, due to the unfortunate way that many researchers chase p-values, these analyses often result in misdirection. That is completely wrong. GWASes have an excellent replication record, and were founded on the basis of stringent p-values precisely because of how earlier candidate-gene studies were garbage due to researchers chasing p-values.
- Real_S 9y ago
  These data can be used to identify their source. This will become easier as more data becomes available. https://news.ycombinator.com/item?id=15209306 https://news.ycombinator.com/item?id=15209306 I guess the value of the data depends on who measures its worth. Replicated p-values lead to multiple publications, which are valuable to academics. But these results can still cause misdirection. What is a low p-value worth if it doesn't lead anywhere?
  - gwern 9y ago
    > These data can be used to identify their source. This will become easier as more data becomes available. Yes, so? (The face paper you link isn't a good example of this anyway, since it's so questionable and re-identification already works much better than that based on stuff like haplotypes.) That's not a real risk, not compared to, you know unlocking the secrets of human genetics. And it has little to do with the research databases: DNA is inherently as far away as it is possible to get from being anonymous, once it started becoming cheap, the loss of genetic privacy was inevitable no matter how it was handled. And it's not that big a deal. We will be much better off for it. > Replicated p-values lead to multiple publications, which are valuable to academics. This is very different from what you were just claiming.
    - rectang 9y ago
      > That's not a real risk, not compared to, you know unlocking the secrets of human genetics. So, it's you who gets to play god and decide to sacrifice individuals for the alleged greater good?
    - Real_S 9y ago
      Unfortunately, GWAS data is unlikely to unlock the secrets of human genetics. We have been in the "post-GWAS era" of genetics for at least a few years now. > And it's not that big a deal. We will be much better off for it. I hope you are right! However, I have doubts. Also, just because sensitive information can be compromised doesn't mean that it should be offered freely.
- sametmax 9y ago
  It's always important to put this in perspective with the human History. There is no place on earth that lived in peace for ever. Not even for a very long time actually. Any country goes back to times were it's at war on it's own territory, or were it's under a dictatorship. It will be true again for France, the US, Canada, Spain, any country. We will go back there, it's an absolute certainty. Maybe not (hopefully not), in our lifetime. But ignoring this is not only wearing blinders, it's a recipe for making it worse. Things like AI, facebook, the NSA intercepting anything, image recognition, cameras in every streets, tracking devices in every pockets and... DNA databases are going to be weaponized against the population. Even if you don't believe in this (which is always strange to me, but for the sake of the argument, I'll have to acceptit), at least consider that it will make any neutral entity in power more likely to become malevolent by giving it the opportunity to access abusable huge power. Hence, if we want to survive and evolve as a specie, we need to deal with those tools carefully, as they are very potent, and this means what they can do for us is as great as what it can do against us.
  - comboy 9y ago
    This is a super interesting discussion. Both sides make good points. I wonder if in the future cost and technology of sequencing will evolve so much that somebody will start harvesting as much data as possible from places like metro, train stations, malls and so on. This would make it inevitable that your DNA ends up in these databases and you just have to accept it. Just like currently one kind of has to accept that thanks to facial recognition getting even better and cameras everywhere one can be tracked even without any electronic devices.
    - deleted 9y ago
      [deleted]
    - sametmax 9y ago
      You don't have to accept it. You can protest. You can explain. You can vote. You can paie for service respecting you. You can educate. Maybe there are others things to do. There is always a choice. Most people saying there is none are just choosing one cost against another and say it's not a choice. Not blaming, i do the same. But we could avoid the disasters, living by thinking about the society ou simple everyday actions produce. However it's not only very hard to do, but most people are not interested in doing so. Or even to consider the question of society, or how to live ones live. Living on auto pilot is one of humanity's biggest problem. It helped us a lot when we were in survival mode, but now that our own construct is the only real danger to our existence, it really is an hindrance.
- rectang 9y ago
  > What privacy risk, exactly? People will eventually be identified individually, as inevitably as the people in the AOL search leak years ago. Then they -- and their blood relatives -- will be associated with negative health traits. And then, companies will discriminate -- in hiring, in insurance... anywhere they can. Because it will be financially advantageous to individual companies even though it is detrimental to society as a whole. Because companies are amoral organisms and it is folly to expect them to behave otherwise.
  - jghn 9y ago
    We're probably no more than a year or two away from a sequenced genome being considered PHI for exactly this reason.
- drewmol 9y ago
  Using the information to assist development of targeted pathogens for biological warfare is an extreme example.
bpicolo 9y ago
Not be the case for everybody, but I'm 100% fine with having my genomic data public, especially in the context of research. That's not to say there aren't potential societal contexts where it would be totally awful (e.g. 1930s Germany) but I can't imagine any risk to myself.
- rectang 9y ago
  Well, I feel sorry for your descendants who won't get hired when it's discovered that they might have inherited BRCA1 and Huntington's Disease from you.
- patall 9y ago
  But thats not the point. The question is whether you can make data public that, while it belongs to you, also belongs (partially) to other people (your siblings, parents, unborn children ...) who might not want to have their genetic data public. Sure, there is may be no risk to you and a data repository like the one described contains an enourmous value for society in the form of biomedical data but that does not mean you have to give it to everyone without knowing their intention. Especially if they end up knowing something about you that you don't.
  - Real_S 9y ago
    This is an incredibly important point! Openly sharing your genetic information makes both you AND your relatives more vulnerable, with vulnerability decreasing as relatedness decreases. It also reveals potentially sensitive information about family traits.
    - jhbadger 9y ago
      That's one (rather selfish) way of thinking about it. Another way of thinking about it is that you (and everybody else) is better off if more genomic data is available for research. It's worth remembering that genomicists like George Church and Craig Venter have made their genomes publically available for all to access.
  - 9y ago
patall 9y ago
> GWAS have proven to be, at best, of little value. In fact, due to the unfortunate way that many researchers chase p-values, these analyses often result in misdirection. I would certainly challenge that, its just that some people considered GWAS as the solution for everything which it clearly isn't, especially because rare mutations where underestimated (and cannot be discriminated in GWAS) and because GWAS was never able to detect the causing variant, just associated/linked genomic loci. And last but not least, the regulatory genome is turning out more and more complex (with interacting variants leading to complexities of O(x^n)) and we do not know yet how it will all be understood, its just that GWAS is one of the better tools we have.

cottonseed 9y ago

I lead the software team in the Neale lab that develops Hail, the software that enabled this analysis: https://hail.is https://hail.is. If you're excited about about applying CS and engineering to enable scientific discovery of massive, fast-growing biological data, get in touch. We just got a bump in funding and we're hiring a number of roles: distributed system database internals, compilers, machine learning, scientific data viz, deployment and operations, and web applications. See our Who's Hiring post: https://news.ycombinator.com/item?id=16288145 https://news.ycombinator.com/item?id=16288145

dang 9y ago
This is off topic outside the Who Is Hiring threads. Discussions here are supposed to gratify intellectual curiosity. It sounds like you're in a position to say a lot of interesting things about this topic! but a job ad isn't interesting.
- cottonseed 9y ago
  Fair, and thanks for clarifying the moderation.

devteambravo 9y ago

That's a terrifying read. See DefCon talk: DEF CON 25 - John Sotos - Genetic Diseases to Guide Digital Hacks of the Human Genome (https://www.youtube.com/watch?v=HKQDSgBHPfY https://www.youtube.com/watch?v=HKQDSgBHPfY)

John_KZ 9y ago
That was absolutely horrific. The worst part was this person calling for a "Apollo-level funded" arms race on developing the most horrific bioweapons possible. If you really care about his problem you should call for a ban on related research and keep yourself silent. The further we delay the development of such technology, the better. Some people argue it's inevitable; Well it's not. For almost 100 years, despite their huge potential in war, chemical and biological weapons have seen almost zero development because of the strict enforcement of the Geneva convention. Let's keep it that way.
- xcvbxzas 9y ago
  I don't think we can confidently say that chemical and biological weapons have seen almost zero development in the last 100 years. We can say as far as we know that's the case, but we also don't have a very compelling reason for knowing. The development of these types of weapons is going to be highly secretive, and not just because of the Geneva convention. Absolutely nothing has gone on in the world in the last 100 years that might tempt the deployment of advanced chemical or biological weapons on any sort of scale. Naturally we haven't seen them used. I also don't see how burying our head in the sand is going to help on this one. At least compared to nuclear weapons, projects on these weapons could be useful for defensive purposes. Everybody is working more or less within the same confines and rules, and I wouldn't be surprised if relatively similar developments were the result. Even if they aren't, the characterization of these weapons can be used to inform and guide the response plans to try to minimize damage in the case of an attack.
  - John_KZ 9y ago
    I have no doubt that biological weapons have been developed to some degree, somewhere, in a well-funded government lab, in complete secrecy. But that is not a problem. This secrecy is what saves us from a race to the bottom. Some government will develop a limited capability of biological warfare. They probably already have. With no information about what their adversaries are doing, they will simply stop. As far as they know, they have developed a state-of-the art biological weapon system, and they are probably correct. One of the reasons that the nuclear arms race happened, was the "openness" of the competition. You can't hide a nuclear explosion. Your adversary knows how sophisticated you are, and they now have to push 1 step further. Biological warfare doesn't have to be like this. Be sure that some Darpa or DoD funded secret project is working on countermeasures, but there's another interesting thing: You can stop biological attacks by quarantine. It's very simple, very effective, and doesn't require developing Armageddon-tier weapons in the process. Another issue that's purposefully isn't discussed in the video is how effective the delivery of these weapons are. Simply put, not very. Viruses, the main attack vector, change in every iteration. There's no guarantee you can infect that many people with an intact version of your weapon. Sooner than later, you genocidal weapon will stop being so selective, because it's evolving for it's own benefit, not yours. And finally, if you really are concerned about this issue, as you should, the right way to fight against it is to find a way to stop the infection and proliferation, to find ways to stop these attacks without accelerating weapons development. There are ways to fight these weapons without building them, and you can definitely do better than starting a public campaign that asks people to develop horrific bioweapons just so we can find a way to stop them later on, maybe.

geobourazanas 9y ago

Hey all, we are a team working toward democratising genetic testing. We are trying to gauge how much people know about genetic testing and what people feel about it. I have a super short form (4 questions only). Would really really appreciate some input from the good folks on this channel! https://joannavass.typeform.com/to/Vy18OL https://joannavass.typeform.com/to/Vy18OL

bob4444 9y ago

I hate to sound like a shill, but this sounds similar to an area Encrypgen (DNA) is trying to reach. (https://encrypgen.com/ https://encrypgen.com/)

lerie82 9y ago

API would be nice