I Built a Private Genomics Study with Stoffel MPC

I Built a Private Genomics Study with Stoffel MPC(vishakh.blog)

21 points by vishakh82 3 hours ago | 22 comments

mfld 21 minutes ago |

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.

vishakh82 10 minutes ago | |

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

badcryptobitch 1 hour ago |

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

usernametaken29 2 hours 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 2 hours 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 2 hours 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 2 hours 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

intheitmines 1 hour ago | | |

Have you used them? Interested myself

mishellaneous 49 minutes ago | |

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?

optionalsquid 2 hours 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 2 hours 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 2 hours ago |

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

cinntaile 2 hours ago | |

Nowadays people would have guessed it was Model Context Protocol.

doctorpangloss 1 hour 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 1 hour 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.

doctorpangloss 51 minutes ago | | |

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.