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NinjaPCR's fight with COVID 19

Shingo Hisakawa edited this page Jul 1, 2020 · 19 revisions

Updates : My presentation at Virtually Maker Faire 2020 introducing NinjaPCR/LAMP/qPCR (2020 May 23 )

Updates : NinjaLAMP released as byproduct and successfully worked with positive control synthesized oligo at Columbia University, NY (2020 Apr 25 )

We are upgrading NinjaPCR into Open-sourced easy-to-use affordable Real-Time PCR. Typical commercial Real-Time PCR costs more than USD20K-200K and our current target kit parts price is USD300 or less. THAT MUST BE USED UNDER CONTROL (ex. official tests in developing countries) not to make too long lines at hospital. How? Let me list facts, plans and need help.

Facts

  1. Real-Time is in need : Typical thermal cycler including current NinjaPCR can be used to test COVID-19 but too many post-processes including electrophoresis are required and that wastes time. So Real Time PCR is mainly used in official tests.

  2. More sensitive than immunochromatography in exchange for risk of contamination : less than 100 virus RNA is enough to detect while immunochromato needs more than 10^4. Even though immunochromato is cheaper and faster, it cannot be used in early stage. That's reason why both are irreplaceable. Sometimes Real Time PCR is too sensitive and easily amplify contaminated RNA that may induce a panic if people without proper knowledge overissue self-test.

  3. Multipurpose : Real Time PCR can be used to test not only COVID-19 but also most of all infectious diseases and others like meat detection, food allergens.

Why NinjaPCR is closest to the goal

Because our NinjaPCR is only one thermal cycler in the world that completes these features.

  1. Open sourced under GPL v3 license : Everything is open, anyone can use but it must be opened too.

  2. Most precise temperature control with thermal simulation model : Thermometer on PCR tube holder or heater is not enough.

  3. Support WiFi : PC is not needed. You can use it with iOS/Android phones. That doesn't mean you need internet. Access Point Mode is ready for offline usage.

Plans

  1. Support at least FAM that's enough to detect COVID-19. Multiplex is better.

  2. WiFi and thermal simulation model will be inherited.

  3. No more peltier. It looks like miniPCR covering from room temperature to 100℃.

  4. Chai qPCR (Apache License v2.0) is 6 year old project. Ours should be more challenging but no idea what's in need.

  5. I think everything should be opened under GPL v3 instead of Apache License v2.0 to keep things opened.

  6. We will rewrite console from scratch with event-driven modern programming language instead of infinite loop.

  7. Support 8 x N tubes.

Need Help

  1. Donation : To compare the results, we must buy commercial Real Time PCR(s) that costs more than 10 to 100 thousand dollars per each (Wow). Expendables for Real-Time PCR are also more expensive than usual thermal cycler. If you kindly let us use yours or donate, it's really helpful. We're currently based in Tokyo Japan. We are accepting donations through One-Time PayPal or Monthly Patreon (Shingo and Mariko).

  2. Discussion (Social) at BioClub Tokyo Slack Channel #ninja-qpcr : How to avoid misleading and panic I'm fed up with. I think EVERY knowledges including each step, how to make required facilities (ex. room with bio safety level 2, depressurized room, autoclave) should be opened together but that exceeds our limit.

  3. Discussion (Technical) at BioClub Tokyo Slack Channel #ninja-qpcr : As Plans4, I need comments and advises from frequent Real Time PCR users. What kind of features shall I add to/cut from Chai qPCR?

  4. Factories (maybe in China) : Small but custom mold for film heater is required. I wish friends in Shenzhen give me a help. Custom shaped filter glass, aluminium CNC is also welcomed.

  5. Tools : We already have metal CNC (for tube holder) and Ultimaker2+. Need access to laser cutter (for cutting MDF board) and high resolution resin printer like Form2 (for mechanical parts) in Tokyo.

References

  1. NinjaPCR : thermal cycler we made deriving from OpenPCR. (Open sourced / Kit / USD499)

  2. Chai qPCR : Real Time PCR (Open sourced / Assembled / USD4499-)

  3. miniPCR : thermal cycler (Close sourced / Assembled / USD650)