DNA sequencing/barcoding

Gerrit

After we discussed how useful it would be to be able to identify different microbial species during last night's journal club, I remembered that DNA sequencing is something that is possible to do at home.

There are two UK companies, Bento Bioworks and Oxford NanoPore Technologies, that make the equipment necessary to do mobile DNA sequencing, so that you can even do DNA barcoding on a boat:

Bento Lab (£1299)
NanoPore MinION (£900)

In short, you use the Bento Lab's centrifuge to extract the DNA, it's PCR to amplify the DNA, and the gel electrophoresis to verify that it worked. Then you use the MinION to actually sequence the DNA.

Obviously it's not quite as simple as that, but the point is that it's not out of reach for the home lab. There are open-source options out there for PCR(e.g. OpenPCR), centrifuges and gel electrophoresis as well. I'm not aware of an open-source nanopore sequencer though.

Martin

Gerrit It's taken me until now to work out who it was that I'd heard speak from Oxford NanoPore Technologies. We edited a video for the Water Action Platform way back during lockdown of a presentation that they made to Isle's Technology Approval Group. I've now reached out to the presenter.

Bento Lab looks really interesting too, I hadn't come across that before, but love their knowledge hub.

Given our open nature, I'm always drawn to Open Science Hardware:

Centrifuges

OpenFuge with a $200 BoM back in 2013 initially looked promising but the inventor's last reply there was 10 years ago.

The presumably closed source SciSpin Fixed speed 7,000 RPM / 2,680 g micro centrifuges are available for £90 and I might put centrifuges in the same category as autoclaves for open source sellers - too dangerous if something goes wrong.

That said, Frank of Africa Open Science Hardware (with whom I had a great conversation after the last GOSH Roadmap co-working session) was looking to develop one. I'll ask him if he's made any progress or if the FOSH Polyfuge (with last commit 3 years ago) is still the latest / best open source option.

PCR

OpenPCR's last software commit was 5 years ago, and the $499 buy now link on OpenPCR.org now takes you to the $5,799 Open qPCR replacement whose last commit was 9 months ago.

PocketPCR seems to be getting most love in the GOSH forum and has a €99 kit - I'm guessing from their GitHub that it's more a product finalised by Gaudi 3 years ago than a thriving open source community.

Gel Electrophoresis

Gel electrophoresis instructables similarly suffer from the last author response being 11 years ago.

openPFGE looks more promising with the last commit only 1 year ago. They say "It costs USD ~$500" although their 2020 HardwareX article's ~$850 may be more recent.

Tobey mentioned in the GOSH forum that IORodeo sold open source high-voltage supplies, gel-chambers and transilluminators - I'll ask Jo if they still do, or what they used to sell for.

DNA Sequencing

Is ReSeq relevant?

I think we should probably ask our friends at GOSH if I've missed the killer projects, like OpenFlexure is for microscopy - with a massive active community & dedicated core developers.

Gerrit

Martin I still have all the bits and pieces to build a centrifuge from the Biohack Academy. I just never got around to it as I didn't have a use for it.

Do you want to add your findings to the Amybo wiki?

Martin

Gerrit yea, I should do - just not convinced we've reached any conclusions on any of the items yet...

Martin

I got a reply from Jo at IO Rodeo:

So, we stopped making and selling our gel electrophoresis and imaging line of products a few years ago. We ran into a sourcing issue with the blue LEDs we were using for the transilluminator. Basically, the quality control on the parts we received became unreliable which significantly increased the time we had to spend on manufacturing, quality control and testing. As we had trouble finding a good replacement part at a similar price point, we made the decision to stop selling them until we could work on a redesign. We also made the decision to discontinue making gel boxes and power supplies at the same time and focus on other areas of product development. We may bring back the transilluminator and electrophoresis power supply if we can find time to do the needed redesigns. We have all the links to the products on Instructables and in our archive which is currently not live. We are in the process of moving those to Github.