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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

#171

Post by Malp »

netizen-936824 wrote: post #16
Malp wrote: 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?

I wasn't thinking sequencing but rather comparison. Could even hash data for comparison to enforce privacy (unsure how effective that would be) But this could enable things like finding relatives which is what I got out of the comment about 23andme. Instead of all the data being centralized, storage and comparison could be distributed

Ah, thanks for clarifying. I misunderstood the main idea behind your comment.

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

#172

Post by petters »

sllabres wrote: post #163
petters wrote: post #159

Earlier quoted context omitted.

This does not seem true? Even if the complete genome of my mother and father is known, there is still a lot of uncertainty left.

Isn't that quite similar to help solving cold cases as example: https://en.wikipedia.org/wiki/Joseph_James_DeAngelo On April 24, 2018, authorities charged 72-year-old DeAngelo with eight counts of first-degree murder, based upon DNA evidence; investigators had identified members of DeAngelo's family through forensic genetic genealogy .

You don't have to reconstruct the genome in order to prove relationships or find a person.

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

#173

Post by thrashh »

emteycz wrote: post #155
andrewxdiamond wrote: post #146

Earlier quoted context omitted.

Subprime mortgages aren’t illegal? Insurers have auditing requirements to prove what goes into the policy calculation. It is impossible to hide illegal data use at any meaningful scale, and no insurance agency is looking to save a buck on a small number of clients. Your comparison is irrelevant.

Illegal or not, look what happened after 2008. Clearly regulation has failed, so there is no reason to think it won't fail in the case of DNA data.

There was never regulation to begin with.

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

#174

Post by godelski »

tekproxy wrote: post #130
adabaed wrote: post #36

Earlier quoted context omitted.

Imagine insurers refusing to give you a service due to your predisposition to certain diseases...

Imagine gene therapy to fix the problems. After a few generations, many diseases will be extinct. There's a guy on YouTube doing diy gene therapy to treat his lactose intolerance so it's not exactly science fiction.

I'm pretty sure the effect was temporary and he had to do it a second time. It's very important to note that this research is still very new and he was lucky that his genetic code was prime for that test. (I'm not against bio hackers btw. I think they provide a very good service though obviously more risky. No problems when that risk is on yourself but just trying to say "don't try this at home").

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

#175

Post by godelski »

jcims wrote: post #137
tekproxy wrote: post #130

Earlier quoted context omitted.

Imagine gene therapy to fix the problems. After a few generations, many diseases will be extinct. There's a guy on YouTube doing diy gene therapy to treat his lactose intolerance so it's not exactly science fiction.

The Thought Emporium https://youtube.com/c/thethoughtemporium He’s got a ton of other interesting projects, the DIY gene therapy is just one that stands out because it seems so risky.

I'm pretty sure he had a second video on how the effects started to ware off.

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

#176

Post by russdill »

petters wrote: post #159
russdill wrote: post #68

Earlier quoted context omitted.

In the near future (or arguably now depending on your purpose) you don't even need that. Assuming enough of your relative's sequences are available, the probability of you having certain genes/mutations can be narrowed down so much that having your individual genome doesn't add much.

This does not seem true? Even if the complete genome of my mother and father is known, there is still a lot of uncertainty left.

Lets say there's some rare genetic disorder, only a few hundreds of a percent of the population has it. If someone knows that your mother or father has it, you now don't have a few hundreds of a percent chance of having it. Depending on the disorder you having it might just be a cointoss.

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

#177

Post by jjeaff »

kortilla wrote: post #148
andrewxdiamond wrote: post #140

Earlier quoted context omitted.

Because insurance is regulated against this. They can’t just Willy-nilly get data and “scores” from uncontrolled sources.

Oh sweet summer child. The astute business person will construct a score that happens to correlate with these known genetic defects and then sell it to insurance anyway with the plausible cover correlated source.

That really isn't how most health insurance works in the US now. As far as I know, there really is no such think as refusing health insurance to an eligible person. Now other types of insurance like life, home, auto, those are a different story. But regular health insurance just has to accept your application.

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

#178

Post by emteycz »

thrashh wrote: post #173
emteycz wrote: post #155

Earlier quoted context omitted.

Illegal or not, look what happened after 2008. Clearly regulation has failed, so there is no reason to think it won't fail in the case of DNA data.

There was never regulation to begin with.

I am absolutely sure there is no one who would call mortgages "unregulated" in 2008. That the regulation is insufficient was determined later - and way too late.

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

#179

Post by lawrenceyan »

joshuamcginnis wrote: post #169
lawrenceyan wrote: post #134

Earlier quoted context omitted.

Given that the decoder is machine-learned and depends on a training set to go from squiggle -> ATGC..., how do you ensure that sequences which haven't been seen before (not in the training set) are still accurately accounted for?

We used Guppy for basecalling, which is neural network based and used to turn raw signal data into the predicted bases. There're no guarantees of accuracy, only tools to determine and assess quality. One major way of assessing accuracy is to compare the subject genome with other similar reference genomes and denote the high-degree of homology in highly-conserved regions.

My question is if in the future, we would be able to fully rely on translations to predicted bases for sequencing or if there would always be a need to compare with a different sequencing methodology in the case of de novo genetic information that previously hasn't been seen before (no reference genomes being available in that case).

Is there publicly available information on how accurate Guppy is, as well as how the amount of training data scales with improvements in accuracy?

It didn't seem like these things were mentioned explicitly in the Community Update, other than that it’s expected to continue improving, but a clearer roadmap would definitely be much more helpful.

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