4 ms·

Can this be used to make faster corona virus tests ? If so maybe this is the time to Manhattan project this technology.

koeng 6y ago
Generally, yes absolutely. I’ve been doing a project called “NanoSavSeq” (Nanopore Saliva Sequencing) in my free time. It’s published on dat right now since the raw files for Nanopore are really big (got too big for hashbase). There is one company doing it as well, but my version is completely open source and I’ve optimized it for affordable automation. To give you a sense, you can buy one for 1k and do as much detection as a 64k device, and it’s small enough to fit in a backpack. One device should be able to do 500-1000 tests per 24hrs at a cost of about $10 per test, not including labor.
- iameoghan 6y ago
  Would love to know more. This is fascinating.
  - koeng 6y ago
    The dat website is at dat://aaca379867bff648f454337f36a65c8239f2437538f2a4e0b4b5eb389ea0caff You can visit with the beaker browser, or share it through dat so it won't ever go down. You can also visit it at http://www.nanosavseq.com/ http://www.nanosavseq.com/ (DNS is not up yet, http://167.172.195.83/book/index.html http://167.172.195.83/book/index.html is direct) It's embarrassingly barren right now, mainly since I've encountered some big problems with getting my DNA quantifier out of storage to start doing a lot more experiments. I'm getting that on Tuesday, so will be updating site then.
    - unixhero 6y ago
      The book / documentation is very clean and presented in a fantastic way. May I ask what engine you are using for presenting this book?
      - koeng 6y ago
        mdbook! By the folks making the Rust docs. I love their formatting.
    - azureus 6y ago
      Would you like to work together on this? This is very interesting stuff.
      - koeng 6y ago
        Would love to. Feel free to email me at koeng101<at>gmail.
- Gatsky 6y ago
  Is this with multiplexing? Or are you extending the flowcell life?
  - koeng 6y ago
    Multiplexing. I use barcoded primers to amplify the sample, then pool and sequence
deleted 6y ago
[deleted]
a_bonobo 6y ago
The Oxford Nanopore people announced that they are in the 'advanced stages' of developing their own Covid-19 test called LamPORE https://twitter.com/nanopore/status/1263711292868694021 https://twitter.com/nanopore/status/1263711292868694021 Press release: https://nanoporetech.com/about-us/news/oxford-nanopore-technologies-announces-advanced-development-lampore-rapid-highly https://nanoporetech.com/about-us/news/oxford-nanopore-techn... 'Oxford Nanopore is planning to deploy LamPORE for COVID-19 in a regulated setting initially on GridION and soon after on the portable MinION Mk1C.' The GridION is still expensive and not affordable for a business or private person, a MinION definitely is.
- koeng 6y ago
  Thanks for those links! I knew it was only a matter of time There are lots of folks working on LAMP in the DIYbio community. The kinda cool thing is that you can just have a colormetric read-out, so you don't even need Nanopore sequencing. I'm guessing that the reason Nanopore is nice there is to eliminate false positives. I'm more a fan of this approach - https://www.genomeweb.com/business-news/clear-labs-raises-18m-will-launch-diagnostic-nanopore-sequencing-covid-19-assay-system https://www.genomeweb.com/business-news/clear-labs-raises-18... Because you can recover full genomes as a by-product of diagnostic tests (which is useful for tracing infection, for example https://nextstrain.org/ https://nextstrain.org/)

Generally, yes absolutely. I’ve been doing a project called “NanoSavSeq” (Nanopore Saliva Sequencing) in my free time. It’s published on dat right now since the raw files for Nanopore are really big (got too big for hashbase). There is one company doing it as well, but my version is completely open source and I’ve optimized it for affordable automation. To give you a sense, you can buy one for 1k and do as much detection as a 64k device, and it’s small enough to fit in a backpack. One device should be able to do 500-1000 tests per 24hrs at a cost of about $10 per test, not including labor.

iameoghan 6y ago
Would love to know more. This is fascinating.
- koeng 6y ago
  The dat website is at dat://aaca379867bff648f454337f36a65c8239f2437538f2a4e0b4b5eb389ea0caff You can visit with the beaker browser, or share it through dat so it won't ever go down. You can also visit it at http://www.nanosavseq.com/ http://www.nanosavseq.com/ (DNS is not up yet, http://167.172.195.83/book/index.html http://167.172.195.83/book/index.html is direct) It's embarrassingly barren right now, mainly since I've encountered some big problems with getting my DNA quantifier out of storage to start doing a lot more experiments. I'm getting that on Tuesday, so will be updating site then.
  - unixhero 6y ago
    The book / documentation is very clean and presented in a fantastic way. May I ask what engine you are using for presenting this book?
    - koeng 6y ago
      mdbook! By the folks making the Rust docs. I love their formatting.
  - azureus 6y ago
    Would you like to work together on this? This is very interesting stuff.
    - koeng 6y ago
      Would love to. Feel free to email me at koeng101<at>gmail.
Gatsky 6y ago
Is this with multiplexing? Or are you extending the flowcell life?
- koeng 6y ago
  Multiplexing. I use barcoded primers to amplify the sample, then pool and sequence

deleted 6y ago

[deleted]

a_bonobo 6y ago

The Oxford Nanopore people announced that they are in the 'advanced stages' of developing their own Covid-19 test called LamPORE https://twitter.com/nanopore/status/1263711292868694021 https://twitter.com/nanopore/status/1263711292868694021 Press release: https://nanoporetech.com/about-us/news/oxford-nanopore-technologies-announces-advanced-development-lampore-rapid-highly https://nanoporetech.com/about-us/news/oxford-nanopore-techn... 'Oxford Nanopore is planning to deploy LamPORE for COVID-19 in a regulated setting initially on GridION and soon after on the portable MinION Mk1C.' The GridION is still expensive and not affordable for a business or private person, a MinION definitely is.

koeng 6y ago
Thanks for those links! I knew it was only a matter of time There are lots of folks working on LAMP in the DIYbio community. The kinda cool thing is that you can just have a colormetric read-out, so you don't even need Nanopore sequencing. I'm guessing that the reason Nanopore is nice there is to eliminate false positives. I'm more a fan of this approach - https://www.genomeweb.com/business-news/clear-labs-raises-18m-will-launch-diagnostic-nanopore-sequencing-covid-19-assay-system https://www.genomeweb.com/business-news/clear-labs-raises-18... Because you can recover full genomes as a by-product of diagnostic tests (which is useful for tracing infection, for example https://nextstrain.org/ https://nextstrain.org/)