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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

#161
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.

It’s not exactly DIY but there are in theory ways to ‘encrypt’ your DNA before it gets sequenced. Something like amplifying/enzymatically modifying the DNA in a way that changes the sequence which you can undo computationally once you get the data back.

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

#162

> Why not make the software into a proprietary product? ... There’s such a race there that it’s hard to commercialize the software for the long term.” Schatz continues, “Plus our work is largely funded through government sponsored grants, so this is one of the important ways for us to give back to society.” In some people's thoughts, making a better society is the first and most obvious thing to do with technology li…

It’s a weird quote anyway since there is commercial, proprietary software for DNA sequence analysis. Just a few examples of companies in this space are Sentieon, Edico (acquired by Illumina) and Parabricks (acquired by Nvidia). And Michael knows this (they’re sufficiently well known, and his own research laid some of the earliest foundations that Parabricks would ultimately build upon) so I’m assuming the quote was taken out of context or he was talking specifically about his own lab.

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

#163

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.

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.

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

#164

Earlier quoted context omitted.

Tl;Dr: Nanopore data is historically lower quality than current gold-standard methods, but it is by no means "not viable" in a genomics pipeline. Their newer chemistry flowcells are competitive with current gold-standard (but I've not seen it with my own eyes in the lab yet due to limited release). There are two components that drive sequencing error rate. 1) The chemistry behind the sequencing (for nanopore sequenci…

Thanks - fascinating stuff. I'm now even more convinced I want to give it a try, but I think I'll play around with public data and tutorials before leaping into home sequencing.

You totally should, it's a lot of fun. I'd suggest trying to find some bacterial genome sequencing (like E. coli) done on nanopore if you're interested in those data. I don't have a link to any handy right now, otherwise I'd post here, but assembling bacterial genomes is shockingly easy these days and doesn't need near as many resources as doing a human genome, so it's great for learning (I love the assembler Flye [1] for this).

And RE: home sequencing, honestly the hardest part for a beginner will likely be the sample prep, since that takes some combination of wet lab experience and expensive equipment. I really wish molecular biology was as simple to get hacking on as writing software. The lag time between doing an experiment and getting a result is so much longer than waiting for things to compile, it just makes improving your skills take longer.

[1] https://github.com/fenderglass/Flye

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

#165

Alas the information presented is an over simplification of the process. To actually sequence DNA with this USB thingy you need to prepare a so called sequencing library - and for that you need a fairly well equipped lab - expensive reagents and years of practice and skill ... a mid level biology Ph.D can prepare these ... in addition the flowcell sold by Oxford Nanopore often malfunctions and the whole run is a bust…

Yep

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

#166

Earlier quoted context omitted.

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 i…

> Looking at the US healthcare system, it's obvious that many doctors' and nurses' talents are wasted doing bureaucratic paperwork. This is incorrect. Most of the paperwork is done by administrative staff. Paying for that giant staff + the actual medical professionals is why things are so expensive. Hospitals are not stupid, they won’t waste their most valuable resource (healthcare time) on bureaucratic paperwork.

An oncology department I'm familiar with has an entire "nurse navigator" whose whole job is to submit "prior approval" requests to "insurance" companies justifying why patients need a specific treatment, plus the nurses employed by the "insurance" companies reading those requests. I believe it's similar for any moderately expensive specialty. A common career path is care nurse -> burnout -> administration. Most of the administration is made up of people who could be providing healthcare.

And no, hospitals' most valuable resource are their billing computers. I think when it comes to providing actual healthcare hospitals are very stupid. You cannot partition any knowledge worker's attention into 10 minute blocks and expect them to achieve anything useful, yet that is what their entire system is designed around. The hospital doesn't have unilateral say of course (an "insurance" company won't pay one doctor the "price" of two if they spend twice as long with a patient), but they're still content optimizing within that status quo outcome - completely scatterbrained care.

And it's not like individual doctors are well rested or happy when you talk to them. The system clearly takes their toll on them (eg disappearing for 5 minutes to go retrieve test results that didn't show up before your appointment). In fact I'd say the vast majority of human talent in the medical system ends up completely wasted.

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

#167

Earlier quoted context omitted.

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.

GC rich regions as in hairpin loops? How would the sequencer deal with those?

If I'm not mistaken the nanopore tech unwinds double-stranded DNA during the reading, so I don't think hairpins are the issue.

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

#168
post #89

Earlier quoted context omitted.

The instruments do exactly as you say (run the sample N times), but this obviously comes at a cost. Also, keep in mind that sequencing needs to be very, very accurate to be useful. We share most of our DNA, and the small variations make up all the difference.

what cost do you mean? time/electricity? reagents? or the cost of someone else charging more for more reads?

Yes, those are all relevant costs. There's also a tradeoff between accuracy and the number of reads (how many sequences you can observe), or how much data you can get out of the machine.

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

#169

Earlier quoted context omitted.

That's not true. I just did a high-quality sequence and assembly of a new species of fungus from my home lab using nanopore. You can see all my code used for assembly and analysis that will be referenced in a paper I plan to publish in Jan here: https://github.com/EverymanBio/pestalotiopsis

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.

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

#170
post #142

Earlier quoted context omitted.

That's not true. I just did a high-quality sequence and assembly of a new species of fungus from my home lab using nanopore. You can see all my code used for assembly and analysis that will be referenced in a paper I plan to publish in Jan here: https://github.com/EverymanBio/pestalotiopsis

I thought I recognized your name from the side hustle story. :) This is super cool!!!

Thanks man!
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