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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

#31

Post by biophysboy »

AstroDogCatcher wrote: post #12
ampdepolymerase wrote: post #6

Earlier quoted context omitted.

A used laboratory grade NGS system can be had for less than 10K https://www.ebay.com/itm/265148387179 Nanopore is still not quite ready yet for precise and high accuracy sequencing. Give it another five years.

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…

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.

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

#32

Post by jacquesm »

DoctorOW wrote: post #24
biophysboy wrote: post #21

Earlier quoted context omitted.

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?

Your DNA can tell you a lot about what could happen, but not about what is happening.

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

#33

Post by LinuxBender »

inciampati wrote: post #23
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?

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.

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

Music is exactly the same notes, just a unique mix. So why is Sony upset that I want to stream their entire library? But jokes aside...

A few decades ago I fought the military on collecting my DNA. I stalled them long enough to get my honorable discharge and avoid that all together. It's funny you ask because the commander asked the same thing and joked "Are you afraid we are going to clone you?!" to which I replied, "No sir, you should be afraid you are going to clone me." and we both had a laugh because he knew I was right. The military are not fond of critical/free thinkers. One of me was plenty. I explained that insurance companies were already using this data to retroactively cancel peoples policies even if they were not actively afflicted by something. The commander showed me how to use the FOIA request system.

Laws have evolved a little since then but there are plenty of other risks. For starters, I can't easily change my DNA like I can change my debit card. That data can be used to tie me to others or guilt by association which is undesirable drama. It can also be used to try to sell me things. It can also be used to target biological weapons against specific groups of people. There appears to be an imbalance of data sharing in this regard. [1] Then there is simply the matter of privacy. If I want to share my DNA with some lab that is in turn going to sell it out to hundreds of other companies over and over forever, I should at very least be getting paid a vast amount of money and land and have legally binding contracts and NDA's that cover what is and is not allowed to be done with my data and how long it may be retained. That contract and the laws enforcing the contract must have some serious teeth with very serious ramifications for anyone violating it whether intentionally or by mistake.

[1] - https://www.youtube.com/watch?v=biNxl7tiVSY

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

#34

Post by Lev1a »

kingcharles wrote: post #29

So, how long before I can take my DNA "ROM" file and boot it in an emulator that would allow it to grow?

An idea just popped into my head reading your comment:

What if you could take the (binary) data file of your DNA and use it as input in the (recently remastered) Monster Rancher games to generate a monster? Apparently those games use external user-provided data (like music CDs, game discs etc.) to generate the monsters the player would then train and use (something I only recently learned about through gaming livestreams).

I'd actually like to see the level of jank that would come out of something like that.

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

#35

Post by rumblerock »

m12k wrote: post #25
biophysboy wrote: post #21

Earlier quoted context omitted.

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.

Years ago I used Ancestry, then requested the .txt file and asked them to delete it from their records. Uploaded it to run a report at https://promethease.com/ that cross-references your SNPs against the existing body of genetic research.

The results have been pretty astounding. I found markers that pointed to poor response to a specific blood thinner my grandfather was put on before he passed. Currently I'm researching the cluster of Bipolar / ADHD / SAD symptoms I experience that all seem to trace back to a certain genotype of circadian rhythm genes I have (thank you, Sci Hub). To boot, some of the studies I've come across have been done on Han Chinese populations that match my descendance.

Perhaps going too far down this rabbit hole poses a self-diagnosis risk, but the correlations to my family history and my own life experience working with doctors to diagnose and treat symptoms are pretty undeniable. And given that your run-of-the-mill psychiatrist is going to treat you off of a DSM checklist, I feel much more confident knowing there have been genomic studies to back things up, since my doctor isn't up to date on this research, and finding one that would be will be difficult and expensive. I've shared the papers with my doc and he's been supportive, sometimes I feel like I should be getting a discount on services rendered.

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

#36

Post by adabaed »

m12k wrote: 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.

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

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

#37

Post by rbartelme »

ampdepolymerase wrote: post #6
LinuxBender wrote: post #2

This is very cool. Are there by chance any associated projects that could evolve into something like 23andme but remain entirely within a private network meaning that the data is entirely in the hands of the individual?

A used laboratory grade NGS system can be had for less than 10K https://www.ebay.com/itm/265148387179 Nanopore is still not quite ready yet for precise and high accuracy sequencing. Give it another five years.

Cost/benefit analysis may dictate that, as other posters suggested, you'd be better served to get raw fastq files from a sequencing lab. Even better if you can send the lab a sample and they'll process the extractions for extra $$.

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

#38

Post by joshuamcginnis »

koeng wrote: post #27
fragmede wrote: post #22

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.

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.

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

#39

Post by foobarbecue »

adabaed wrote: post #36
m12k wrote: 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.

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

If you haven't seen Gattaca, you should

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

#40

Post by joshuamcginnis »

ampdepolymerase wrote: post #6
LinuxBender wrote: post #2

This is very cool. Are there by chance any associated projects that could evolve into something like 23andme but remain entirely within a private network meaning that the data is entirely in the hands of the individual?

A used laboratory grade NGS system can be had for less than 10K https://www.ebay.com/itm/265148387179 Nanopore is still not quite ready yet for precise and high accuracy sequencing. Give it another five years.

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
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