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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

#91
post #43

I don't see any reference to the "USB dongle" mentioned in the title. I was thinking this would be some cool thing you could do at home.

https://nanoporetech.com/products/minion

Ah thanks! Not something 'just for fun', so. But good to see this tech is becoming more affordable!

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

#92

Earlier quoted context omitted.

At scale?

I'm curious whether a Covid PCR test could be used to sequence your DNA. Is there enough of a specimen in the process.

Yes, of course there is. Just like any other medical sample you have ever given. Blood, stool, urine, swaps...

But also all the unintentional donations: Every pubic hair you lost on the toilet seat, every tampon you disposed, every bandage you ripped off and threw away, every mattress you slept on, chewing gum you've spit out, every ejaculation, every ... you get the idea.

That's why you need laws to regulate this.

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

#93
post #53

Earlier quoted context omitted.

It's amazing how many problems you avoid by having public health system.

You avoid the problem with medical debt, to be precise. You cannot really avoid the fundamental constraints - anywhere in the world, there are only so many doctors and so much money available for treatments. IDK if USA has a shortage of doctors, but plenty of European countries do. A country like Romania just cannot give its doctors big enough wages to stop them from seeking employment elsewhere, where they will get…

The argument was about "free-market" insurance contracts tho.

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

#94
post #53

Earlier quoted context omitted.

It's amazing how many problems you avoid by having public health system.

You avoid the problem with medical debt, to be precise. You cannot really avoid the fundamental constraints - anywhere in the world, there are only so many doctors and so much money available for treatments. IDK if USA has a shortage of doctors, but plenty of European countries do. A country like Romania just cannot give its doctors big enough wages to stop them from seeking employment elsewhere, where they will get…

That's a pretty poor way of pigeonholing the problem. Looking at the US healthcare system, it's obvious that many doctors' and nurses' talents are wasted doing bureaucratic paperwork. Simultaneously, if there is a genuine lack of healthcare providers, there is no price signal that would encourage more to enter the market.

What you say may be somewhat true in the context of transmuting the US's "private" bureaucracy into bona fide "government". But it's certainly not a "fundamental constraint" that's impossible to solve. Rather it's a failure of organization, whether critiqued in terms of bottom-up market failure or top-down governance failure.

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

#95
post #27

Earlier quoted context omitted.

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.

A qubit or fluorometer isn't required. You can use a simple DNA ladder to measure the relative quantity and quality of DNA that's good enough for nanopore sequencing. I just did a full genome sequence of a novel fungus using this exact approach.

So, for about 1000$ I can sequence my DNA at home without giving the data away?

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

#96
post #48
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.

Note that you are literally shedding identifiable DNA from your body at all times and a truly motivated adversary would have no problem obtaining enough sample material to do high quality sequencing.

One of the key differences is that in the case of the DNA sequencing services, you're agreeing to ToS that allow them to abuse your data (and thus indirectly the data of any of your blood-relatives), and you directly tie the data to a name and address.

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

#97

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-...

Note that Oxford Nanopore seems to have very much a "sell the ink/razor/etc" business model with their devices: that $1,000 package comes with one flow cell, which is a consumable and costs $900. They're essentially giving the device away for free.

On some of their larger devices (eg, the PromethION), they've moved outright to a "we lend you the device for free, you buy the consumables" model.

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

#98
post #54

Earlier quoted context omitted.

Huh, interesting. Did you fragment? I’d imagine comparison of high weight gDNA wouldn’t be too nice on a gel. You also still, in that case, need a gelbox + ladder + loading dye + sybrsafe or whatever, so it’s still not nothing.

I did a HMW extraction kit on the DNA and used a gel to estimate the volume of HMW DNA. Yes, you need to be able to run a gel, but I'm not sure what the expectation is from folks; that you just place a random piece of non-sterile tissue on a chip and have it do the extraction, sequencing and assembly? That seems like an unrealistic expectation.

They do work on an extraction flowcell that can be added on top. I’m hoping they can make it as easy as adding sample to a well, at least for blood or saliva.

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

#100

Earlier quoted context omitted.

At scale?

I'm curious whether a Covid PCR test could be used to sequence your DNA. Is there enough of a specimen in the process.

I read a story[1] about a UK-based Covid testing firm who was planning on collecting and selling their customers' DNA samples.

> Its "research programme information sheet", last updated on October 21, says the company retains data including "biological samples" and "the DNA obtained from such samples", as well as "genetic information derived from processing your DNA sample ... using various technologies such as genotyping and whole or partial genome sequencing".

The policy also says Cignpost may share customers’ DNA samples and other personal information with "collaborators" working with them or independently, including universities and private companies, and that it "may receive compensation" in return.

[1] https://www.telegraph.co.uk/news/2021/11/14/covid-test-firm-...

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