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I Built a Private Genomics Study with Stoffel MPC

vishakh.blog

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Re: I Built a Private Genomics Study with Stoffel MPC

#21

Post by doctorpangloss »

vishakh82 wrote: post #17
doctorpangloss wrote: post #12

It's a very interesting project. What are the big picture goals? I am asking from the POV of having spoken to many people in the genomics data ecosystem, such as pharmaceutical "chief commercialization officers," not just engineers.

Let people get their DNA sequenced without giving up anonymity or privacy. Let people benefit from DNA data analysis without the data leaving their device or sphere of control. Let people monetize their genetic data without compromising their security.

okay, it's interesting that you chose those three goals, i would have picked three very different goals (i support your mission don't misunderstand me). here is an illuminating reason why:

let's say i recorded a video of the ENTIRE end user experience of (A) collecting the genomics data with your solution (B) using an existing solution. which scene in the video would be different?

see, the problem is, not a single scene would be different.

Re: I Built a Private Genomics Study with Stoffel MPC

#22

Post by mishellaneous »

usernametaken29 wrote: post #4

In genetics the end user is never the consumer. You have to collect blood, prepare it, sequence it. These are all highly specialised steps in which something will and can go wrong, and that’s why typically a hospital carries them out. That’s before even getting the device to do sequencing. The cheapest nanopore comes you at a couple ten thousand euros. Given the premise your work strikes me as oddly theoretical. Who…

couldn't this argument could be made against a lot of scientific research? i bet it took a long time for the average consumer to benefit from the discovery of the double helix structure of the DNA.

and the government funds that kind of stuff even. so what's wrong with a private person doing it?

Re: I Built a Private Genomics Study with Stoffel MPC

#23

Post by mfld »

Very interesting project! I can imagine usefulness even beyond the intended use case, namely in joining the information from multiple large genomics studies. The sharing and access of such data becomes increasingly difficult, and by this approach one could increase the effective sample size while keeping the data private.

Re: I Built a Private Genomics Study with Stoffel MPC

#24

Post by vishakh82 »

doctorpangloss wrote: post #21
vishakh82 wrote: post #17

Earlier quoted context omitted.

Let people get their DNA sequenced without giving up anonymity or privacy. Let people benefit from DNA data analysis without the data leaving their device or sphere of control. Let people monetize their genetic data without compromising their security.

okay, it's interesting that you chose those three goals, i would have picked three very different goals (i support your mission don't misunderstand me). here is an illuminating reason why: let's say i recorded a video of the ENTIRE end user experience of (A) collecting the genomics data with your solution (B) using an existing solution. which scene in the video would be different? see, the problem is, not a single sc…

I think I understand what you’re saying.

We’re focusing on an incremental improvement.

There are people actively working on private home sequencing, at home analysis devices, etc and they’re best placed to do it.

We’re trying to get ahead of a near future where people, implicitly or explicitly, are paid for their genetic data in insecure or exploitative ways.

Re: I Built a Private Genomics Study with Stoffel MPC

#25

Post by vishakh82 »

mfld wrote: post #23

Very interesting project! I can imagine usefulness even beyond the intended use case, namely in joining the information from multiple large genomics studies. The sharing and access of such data becomes increasingly difficult, and by this approach one could increase the effective sample size while keeping the data private.

Thanks! And, yes, exactly..MPC can be a boon for such data sharing.

Re: I Built a Private Genomics Study with Stoffel MPC

#26

Post by doctorpangloss »

vishakh82 wrote: post #24
doctorpangloss wrote: post #21

Earlier quoted context omitted.

okay, it's interesting that you chose those three goals, i would have picked three very different goals (i support your mission don't misunderstand me). here is an illuminating reason why: let's say i recorded a video of the ENTIRE end user experience of (A) collecting the genomics data with your solution (B) using an existing solution. which scene in the video would be different? see, the problem is, not a single sc…

I think I understand what you’re saying. We’re focusing on an incremental improvement. There are people actively working on private home sequencing, at home analysis devices, etc and they’re best placed to do it. We’re trying to get ahead of a near future where people, implicitly or explicitly, are paid for their genetic data in insecure or exploitative ways.

if i recorded the video of "private home sequencing," what scene would be different? i suppose you would put the sample collector into some kind of not-yet-existent affordable device? and then what, you get an sd card?

all the value is in the analysis and sharing.

define insecure or exploitative. it is a very shallow argument to say, iNsUrAnCe cOmPaNiEs - genomic data harvested by insurance companies will never benefit the consumer, but we already have laws against that scenario, the technology doesn't really matter. or the narrow situation with, something something, medical research derived from tissues and the tissue-donators not given a just compensation? i don't know if that's exploitative. and people are already walking, insecure DNA-donators. you are surrounded by easily deanonymized DNA samples everywhere you walk right now...

Re: I Built a Private Genomics Study with Stoffel MPC

#27

Post by vishakh82 »

doctorpangloss wrote: post #26
vishakh82 wrote: post #24

Earlier quoted context omitted.

I think I understand what you’re saying. We’re focusing on an incremental improvement. There are people actively working on private home sequencing, at home analysis devices, etc and they’re best placed to do it. We’re trying to get ahead of a near future where people, implicitly or explicitly, are paid for their genetic data in insecure or exploitative ways.

if i recorded the video of "private home sequencing," what scene would be different? i suppose you would put the sample collector into some kind of not-yet-existent affordable device? and then what, you get an sd card? all the value is in the analysis and sharing. define insecure or exploitative. it is a very shallow argument to say, iNsUrAnCe cOmPaNiEs - genomic data harvested by insurance companies will never benef…

Just to be clear, we are not ourselves working on private home sequencing.

I'm aware of people working on at-home devices but that is not our own approach.

We are just working on a mixing service to anonymize data user identities as their samples and data move through labs, logistics, etc.

Legal protections around genetic data can easily be rolled back in several ways, both incremental and drastic.

While it's true someone's DNA can easily be collected by a sufficiently motivated party, there is still a need at scale for something regular people can use to investigate their ancestry and predispositions without becoming datasets for unheeding organizations.

The 23andMe hacks, for example, should be a sobering realization that personal genomics is a systemic risk for several classes of people.

Re: I Built a Private Genomics Study with Stoffel MPC

#28

Post by enbarca »

Very cool PoC for self-sovereign AI! Federated learning across private data resident on user's phone makes sense, but still begs the question of how the user gets access and controls access to their genomic data in a private way. From my perspective, the solution requires giving the user programmatic control over their data, no matter where it resides. At least that's the premise behind work on LifeCare.ID. Let me know if your open to collaborating. https://lifecare.id
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