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Sequencing your DNA with a USB dongle and open source code

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Re: Sequencing your DNA with a USB dongle and open source code

#21
post #18

I'm really curious about what I could learn by getting my DNA sequenced, but I'm worried about my rights to not have it recorded and shared without my consent if I got someone else to do it for me - so any advance toward an affordable home test setup is very welcome.

Its only valuable if somebody also interprets it for you, such as telling you whether you have a genetic predisposition for certain diseases.

Re: Sequencing your DNA with a USB dongle and open source code

#23
post #11

Earlier quoted context omitted.

Sounds like a fediverse project?

Oh God, I would not want a distributed group of actors with limited trust to sequence my DNA. Maybe it's a project for close group of friends that would be interested?

Your DNA is almost exactly the same as other people's, just a unique mix.

Not sure what you are concerned about. What would you expect a bad actor to do with your DNA sequences? I'm genuinely curious.

Re: Sequencing your DNA with a USB dongle and open source code

#24
post #18

I'm really curious about what I could learn by getting my DNA sequenced, but I'm worried about my rights to not have it recorded and shared without my consent if I got someone else to do it for me - so any advance toward an affordable home test setup is very welcome.

Its only valuable if somebody also interprets it for you, such as telling you whether you have a genetic predisposition for certain diseases.

Is that not something software can theoretically provide?

Re: Sequencing your DNA with a USB dongle and open source code

#25
post #18

I'm really curious about what I could learn by getting my DNA sequenced, but I'm worried about my rights to not have it recorded and shared without my consent if I got someone else to do it for me - so any advance toward an affordable home test setup is very welcome.

Its only valuable if somebody also interprets it for you, such as telling you whether you have a genetic predisposition for certain diseases.

One of the other comment threads indicates that the data, that you need to do that kind of annotation of the sequence, is to some extent available for home use as well: https://news.ycombinator.com/item?id=29695449

I'm really hoping someone will work on an open source "23andme@home" solution that ties all this together in an accessible way.

Re: Sequencing your DNA with a USB dongle and open source code

#26
post #11

Earlier quoted context omitted.

Oh God, I would not want a distributed group of actors with limited trust to sequence my DNA. Maybe it's a project for close group of friends that would be interested?

Your DNA is almost exactly the same as other people's, just a unique mix. Not sure what you are concerned about. What would you expect a bad actor to do with your DNA sequences? I'm genuinely curious.

A very practical reason not to want your DNA out there, unrestricted, is insurance costs. From car insurance, to health insurance, to mortgage lending rates, and life insurance, and while GINA from 2008 is supposed to protect that information, there are loopholes with the interpretation of that law that should give everybody pause.

Re: Sequencing your DNA with a USB dongle and open source code

#27

I don't know if this is the exact nanopore USB dongle used in the article, but this one is $1,000 for the base package, first released in 2014 https://store.nanoporetech.com/us/minion.html https://www.extremetech.com/extreme/190409-minion-usb-stick-...

Yep that’s the one. They update the flow cells over time. The bit they don’t tell you is the stuff you need, like a qubit, to properly run the thing.

Re: Sequencing your DNA with a USB dongle and open source code

#28

Earlier quoted context omitted.

Interested outsider here; I work with a lot of HCLS research customers but don't have a biology-related background. Can you explain the problems with the Nanopore sequencer accuracy in more detail? Basically, I was wondering if I could get one for myself and sequence my own genome, then user the data to learn about life-sciences computing techniques. If I were to buy one of the USB-attachable devices and run it, is t…

I recommend reading this review https://genomebiology.biomedcentral.com/articles/10.1186/s13... I guess there are limits to ensemble methods if the underlying accuracy doesn't increase. I don't work on gene sequencing algorithms but from what I understand of ML ensemble techniques, there are certain assumptions regarding the underlying independence of the errors. The errors for nanopore should be uniform but I am not…

I know that the error rate of the oxford nanopore sequencer depends on GC content (guanine/cytosine nucleotides), and that the Pacific Biosciences sequencer uses a polymerase that gets worn down during reading. So there is some non-uniformity in the chemistry.

Re: Sequencing your DNA with a USB dongle and open source code

#30
post #11

Earlier quoted context omitted.

Oh God, I would not want a distributed group of actors with limited trust to sequence my DNA. Maybe it's a project for close group of friends that would be interested?

Your DNA is almost exactly the same as other people's, just a unique mix. Not sure what you are concerned about. What would you expect a bad actor to do with your DNA sequences? I'm genuinely curious.

Using that analogy, all the 1s and 0s in your private key are the same as everyone else's as well. Genetic data can be used for all kinds of things, the worst of which would be things like targeted diseases or planting your DNA at a crime scene.
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