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Old 08-02-2019, 09:00 AM   #1
Haiqu
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Default Homebrew gear

Doesn't seem to be a topic heading for this, maybe there should be one so that relevant data can be collected in one place.

There are several projects around for PCR's but very little else. Anyone heard of a DIY sequencer (except for the one I already know about by Alexander Sokolov) or synthesizer?

Good tutorials would also be welcomed. I managed to find a great one on DNA extraction (starts here: https://www.youtube.com/watch?v=tcPgdR9_t64 ) but very little else.

For all the interest in Citizen Science and biohacking, there seems to be quite a dearth of useful information on the basics.

Last edited by Haiqu; 08-02-2019 at 09:03 AM.
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Old 08-02-2019, 09:08 AM   #2
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PCR machines:

https://hackaday.io/project/1864-5-d...icator/details
https://openpcr.org/

Sequencer:

https://hackaday.io/project/160183-d...uencer/details

Tutorials:

http://www.the-odin.com/how-to-get-started/

CRISPR kit:

http://www.the-odin.com/diy-crispr-kit/

Any additions welcomed.
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Old 08-02-2019, 09:13 AM   #3
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3D printed centrifuge:

https://hackaday.com/2016/05/03/dna-...ed-centrifuge/
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Old 08-02-2019, 09:21 AM   #4
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Electrophoresis:

https://hackaday.com/2017/05/11/get-...ophoresis-rig/
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Old 08-02-2019, 03:18 PM   #5
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Those are all super cool, but I think the root of the problem is that sequencers are multiple-fold more complex than any of the other devices. A centrifuge spins fast, PCR heats and cools, but sequencing has to measure "something" on a highly multiplex scale.

Even the sequencer in the above uses existing materials at the core rather than coming up a simple shortcut for "good enough" sequencing. It would be hard to find a sub-$1000 sequencing service provider, even for a small project since the lowest cost run is around that. Maybe a maker space could get an old MiSeq and combine samples from members on a run, but it will need service and calibration.
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Old 08-02-2019, 07:39 PM   #6
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As another user pointed out, a library can be sent to sequencing services to be batched with other work. Until today I didn't know such services were available in Australia, they certainly don't advertise.

The complexity of a sequencer is no worse that many other machines I've worked on (or designed, for that matter.) The hard part is, as you rightly point out, the sensor assembly. Until these are available as an off-the-shelf item, building a sequencer is in the too-hard basket.
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Old 08-06-2019, 06:58 PM   #7
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What would the ideal sequencer look like for the hobbyist?

My postulate for the required features:

1. Cheap to build, but not necessarily simple.
2. Uses readily available, relatively inexpensive and non-proprietary reagents.
3. Utilizes a cheap disposable flow cell, or a reusable flow cell.
4. Smaller than a desktop PC, and preferrably much lighter.
5. As accurate as results from Gen2 technologies (2009 era).
6. No complex alignment, or realignment, to maintain accuracy.

Desirable but unnecessary features:

1. Ability to sequence the human genome. Plenty of cheap services available for this.
2. Speedy results. Hobbyists have more time than money.
3. Not fiddly to operate. For a single machine, a learning curve is acceptable.
4. High resolution. 1x is probably fine, interesting results can be farmed out if high res is required.
5. Simple bioinformatics. The hacker culture can find a way to extract data.

Surely there has been an abandoned technology that fits these criteria ...

Last edited by Haiqu; 08-06-2019 at 07:20 PM.
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