I Built a Private Genomics Study with Stoffel MPC

vvishakh82 about 2 hours ago 16 commentsRead Article on vishakh.blog

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usernametaken29•about 1 hour ago

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 is that mystery home DNA lab that needs decentralised private compute? Also, and funnily enough, for much of the genomic pipelines to run (eg a paternity test or a cancer test), a home computer is sufficient. Again, of course, you would need proper medical training to read, interpret and judge the results, which is why a hospital does it… so what problem exactly are you solving?

vishakh82•about 1 hour ago

There are many motivations for consumer genomics and they might pick up further.

https://vishakh.blog/2025/07/08/using-mpc-for-anonymous-and-...

If you look at a previous experiment we did, the costs for getting genotyped are pretty moderate (<$80) and going down further. Blended genome-exome (<$150) and full genome sequencing (<$500) are getting cheaper as well.

Through our Explorer product (https://explorer.monadicdna.com/) we let people glean information about their genome using GWAS Catalog data.

This PoC addresses the next step, i.e. how to keep genetic data private at the user level while still allowing aggregate studies to happen, with or without financial incentives.

timschmidt•about 1 hour ago

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.

optionalsquid•39 minutes ago

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 expensive, and you have to buy reagents as well: https://www.machinio.com/illumina/dna-sequencers

usernametaken29•29 minutes ago

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.

vishakh82•33 minutes ago

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.

optionalsquid•about 1 hour ago

> Most genomic studies begin by asking participants to upload one of the most identifying and irrevocable pieces of data they own, their DNA.

I'm curious what the author means by "asking participants to upload ... their DNA", because I am not aware of any study that asked participants to do that.

vishakh82•42 minutes ago

You're right, most analyses are done using biobanks, etc right now. The sentence is an oversimplification but people still implicitly contribute their data to insecure and centralized sources.

If we can enable people to get sequenced not just when they are sick but for altruistic or financial reasons without leaking their DNA data, we could unlock much bigger datasets than currently available, especially from populations that are underrepresented or ignored.

thisisauserid•about 2 hours ago

MPC for Multi-Party Computation, not for Model Predictive Control.

cinntaile•about 1 hour ago

Nowadays people would have guessed it was Model Context Protocol.

doctorpangloss•27 minutes ago

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.

vishakh82•8 minutes ago

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.