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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

#11

Post by usernametaken29 »

optionalsquid wrote: post #9
timschmidt wrote: post #5

Earlier quoted context omitted.

https://www.the-odin.com/ $599 for 30x coverage sequencing of any whole genome: https://www.the-odin.com/whole-genome-sequencing-30x/ Or purchase the equipment you need to DIY.

That's a kit for sample collection. You would then ship off your sample to the company in question, and they would do the actual sequencing, and then send the DNA data and genetic variants they've inferred back to you. I think that defeats what the article author is trying to accomplish, since you still share your entire genome with a third party. The actual instruments used by that company are a whole lot more expen…

This! And even if you could magically have a 1000$ sequencer at home, you still need to correctly extract the blood, and apply the kit. It sounds easy but really isn’t, this isn’t home baking but PCR, where it’s easy to mess up. You need to know when a result is a true positive and whether your sample is useful / correctly collected. Maybe an inspired bioinformatics citizen lab can do it, but it’s bizarre to think the average consumer would do it. It’s not as simple as taking a drop of blood beep boop result like it is for insulin tests and I don’t think it’ll be like that for a very long time to come.

Re: I Built a Private Genomics Study with Stoffel MPC

#13

Post by usernametaken29 »

vishakh82 wrote: post #10
optionalsquid wrote: post #9

Earlier quoted context omitted.

That's a kit for sample collection. You would then ship off your sample to the company in question, and they would do the actual sequencing, and then send the DNA data and genetic variants they've inferred back to you. I think that defeats what the article author is trying to accomplish, since you still share your entire genome with a third party. The actual instruments used by that company are a whole lot more expen…

We have shown that we can batch user samples and then send them anonymously to the lab. Users can then use an MPC protocol to securely fetch their data without losing anonymity. We plan to roll out a product called Batcher which does this soon.

So essentially you’re telling people: “Don’t use the evil labs they can read your DNA, instead send DNA to our lab and with magic maths we won’t be able to read your DNA but diagnose you!”

Sounds about right to me

Re: I Built a Private Genomics Study with Stoffel MPC

#14

Post by vishakh82 »

usernametaken29 wrote: post #13
vishakh82 wrote: post #10

Earlier quoted context omitted.

We have shown that we can batch user samples and then send them anonymously to the lab. Users can then use an MPC protocol to securely fetch their data without losing anonymity. We plan to roll out a product called Batcher which does this soon.

So essentially you’re telling people: “Don’t use the evil labs they can read your DNA, instead send DNA to our lab and with magic maths we won’t be able to read your DNA but diagnose you!” Sounds about right to me

Not our lab. We simply aggregate the anonymous samples and then work with third party accredited labs.

Re: I Built a Private Genomics Study with Stoffel MPC

#15

Post by optionalsquid »

vishakh82 wrote: post #10
optionalsquid wrote: post #9

Earlier quoted context omitted.

That's a kit for sample collection. You would then ship off your sample to the company in question, and they would do the actual sequencing, and then send the DNA data and genetic variants they've inferred back to you. I think that defeats what the article author is trying to accomplish, since you still share your entire genome with a third party. The actual instruments used by that company are a whole lot more expen…

We have shown that we can batch user samples and then send them anonymously to the lab. Users can then use an MPC protocol to securely fetch their data without losing anonymity. We plan to roll out a product called Batcher which does this soon.

I'm not sure I understand how that that would make a material difference. The company might not know who submitted each sample, but the company would still have their entire genomes in their possession. That is no different, than if somebody obtained the data from a biobank. The data in biobanks is normally also anonymized, insofar that you can anonymize whole-genome DNA data

Re: I Built a Private Genomics Study with Stoffel MPC

#16

Post by vishakh82 »

optionalsquid wrote: post #15
vishakh82 wrote: post #10

Earlier quoted context omitted.

We have shown that we can batch user samples and then send them anonymously to the lab. Users can then use an MPC protocol to securely fetch their data without losing anonymity. We plan to roll out a product called Batcher which does this soon.

I'm not sure I understand how that that would make a material difference. The company might not know who submitted each sample, but the company would still have their entire genomes in their possession. That is no different, than if somebody obtained the data from a biobank. The data in biobanks is normally also anonymized, insofar that you can anonymize whole-genome DNA data

The idea is to create an incentive or altruistic mechanism for people to contribute their data without losing anonymity and privacy.

Re: I Built a Private Genomics Study with Stoffel MPC

#17

Post by vishakh82 »

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.

Re: I Built a Private Genomics Study with Stoffel MPC

#18

Post by intheitmines »

timschmidt wrote: post #5
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…

https://www.the-odin.com/ $599 for 30x coverage sequencing of any whole genome: https://www.the-odin.com/whole-genome-sequencing-30x/ Or purchase the equipment you need to DIY.

Have you used them? Interested myself

Re: I Built a Private Genomics Study with Stoffel MPC

#19

Post by badcryptobitch »

Founder of stoffelmpc.com here.

Thank you vishakh82 for sharing.

It's great seeing folks apply PETs to key problems, no matter how theoretical they might seem now as evidenced by the comments. PoCs like this are steps in the right direction to make such work and ideas practical.

If any of you are looking to try out Stoffel, you can check out our docs at docs.stoffelmpc.com or go to our github repo: https://github.com/Stoffel-Labs/stoffel

Re: I Built a Private Genomics Study with Stoffel MPC

#20

Post by timschmidt »

optionalsquid wrote: post #9
timschmidt wrote: post #5

Earlier quoted context omitted.

https://www.the-odin.com/ $599 for 30x coverage sequencing of any whole genome: https://www.the-odin.com/whole-genome-sequencing-30x/ Or purchase the equipment you need to DIY.

That's a kit for sample collection. You would then ship off your sample to the company in question, and they would do the actual sequencing, and then send the DNA data and genetic variants they've inferred back to you. I think that defeats what the article author is trying to accomplish, since you still share your entire genome with a third party. The actual instruments used by that company are a whole lot more expen…

Yes, I'm aware. I'm also aware that Oxford Nanopore now sells a $5,150 MinION pack containing the sequencer, five full flow cells, and a sequencing kit. Admittedly it's not targeted at whole human genomes, for which Oxford sells PromethION. But I'm not going to say it couldn't be done. And for much less than the [inflation adjusted] cost of my first computer. Even starting from an empty bench you're looking at $7 - $10k.
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