There are some bio HackerSpace labs with memberships open to the public.
London, UK https://biohackspace.org/
Brooklyn, NY, https://www.genspace.org/
Baltimore, MD, https://bugssonline.org/
Australia, https://foundry.bio/
Sequencing your DNA with a USB dongle and open source code
121–130 of 179 posts
Re: Sequencing your DNA with a USB dongle and open source code
#122Earlier 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.
It is unrealistic but for laymen like me, that's the impression I got from the title.
Re: Sequencing your DNA with a USB dongle and open source code
#123Earlier quoted context omitted.
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.
It's not the motivated adversary I am worried about, who actually has to show up where I have physically been. It is the company on the other side of the world in a country with lax legislation, profiling me based on the data I 'shed' online, like a cloud-based DNA sequencing service.
This is my threat model for most things in life. If someone is physically targeting me, I'm fucked. I'm more worried about limiting the casual long-distance attacker since I have more ability to stop them.
If someone steals my DNA I can't stop them. But I can at least avoid being swept up in large scale DNA scanning and tracking efforts.
Re: Sequencing your DNA with a USB dongle and open source code
#124Earlier quoted context omitted.
Could you please explain how this mapping works? Why it needs so much RAM? Is it doing a fuzzy search of sorts for known sequences (genes)? Why can't it do so one by one?
bwa specifically performs a burrows wheeler transform of a 3GB string. other mapping algorithms usually rely on some sort of indexing of the genome. the program then loads this into memory and queries that index for each “read” (a dna fragment from the dna sequencer). when i worked on https://github.com/iontorrent/tmap we thought it would be a good idea to do something like a “local alignment” (using https://en.wikip…
Human DNA contains roughly 3.2 billion nucleotides. A 3 GB string suggests an encoding with one byte per nucleotide.
I'm curious: since there are only 4 bases in DNA, for genomic data, this seems rather inefficient. Is there any advantage in encoding the DNA with two bits per nucleotide?
source for 3.2 billion: https://www.ncbi.nlm.nih.gov/books/NBK21134/#!po=0.485437
Re: Sequencing your DNA with a USB dongle and open source code
#125Earlier 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
How do you know the quality of the resulting sequence?
You don't, not without either resequencing it with another sequencing system or benchmarking the sequencer with a known sequence.
Re: Sequencing your DNA with a USB dongle and open source code
#126Earlier 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
How do you know the quality of the resulting sequence?
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Re: Sequencing your DNA with a USB dongle and open source code
#127Earlier 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
How do you know the quality of the resulting sequence?
There are quality checks throughout the entire process, starting from the raw read quality scores returned directly from the sequencer all the way to fully assembled genome completeness. In our paper, one of the tools we used for this is called BUSCO[0] which scored our assembly at 97.9%, a relatively high score for de novo assemblies.
Re: Sequencing your DNA with a USB dongle and open source code
#128Earlier quoted context omitted.
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?
You can get a usable partial genome at home using a minion (provided you have access to basic lab equipment and consumables, like pipettes, a microcentrifuge, gel electrophoresis kit) for about $2.5k, and a fairly decent one for $5k (about 22x coverage - not perfect but plenty for most purposes).
Re: Sequencing your DNA with a USB dongle and open source code
#129Earlier quoted context omitted.
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 i…
Capitalism, nepotism, public, private, insurance, nationalised healthcare ... the GP is saying that these are methods of dividing up available care, not methods for creating more available care.
X is the amount of medical care available
Y is the amount of medical care wanted
If Y If X > Y it doesn't matter which system you choose, someone will go without. You can change who goes without but you cannot fix the system by changing the method of dividing care.
Can things be somewhat improved with better organisation? Sure. Probably. But let's not overestimate it either. Let's take a dream scenario: optimal organisation can make 20% more care available. How much more care is wanted? I think we can safely say the US population wants 200% or more than the current system provides. Whilst nobody's opposed to improving organisations, it cannot fix the problem.
Fixing the problem is something you can only do by doubling the medical training available. That'll be a lot of extra dollars, none of which go anywhere near patient care for at least 10 years, so I would expect a lot of strong opposition from a lot of sides. But it's the only way to fix things.
Re: Sequencing your DNA with a USB dongle and open source code
#130I'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.
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.