Real Time PCR (qPCR)LAMP (Loop-mediated isothermal amplification) and thermal cycler (PCR) machines are essential tools used for COVID-19 testing.

This is my 20 minutes presentation at Virtually Maker Faire 2020 on May23. This article is updated on Aug28. Latest updates are added to the bottom.

PCR is essential

After COVID-19 pandemic, "PCR" is well-known word as testing method but it's not only for COVID-19. That's biological technique to get enough copies of specific part of DNA to see with naked eyes or fluorescence light sensors. DNA is too small and we cannot observe any results without PCR process.

By changing reagents, PCR machine can be used for any kinds of DNA testing including Malaria (200M people infected, 400K killed every year), food allergen (200K people needs in US), Science education, criminal investigation, paternity test and so on.

You may heard about other testing method like immunochromatography and antibody test. Here's pros and cons of all methods and these technique cannot replace PCR.

  • Immunochromatography : Cheap (<USD10/disposable shot) but less sensitive than PCR. Need more volume of virus sample than PCR and cannot be used for patients in early stage of infection.
  • Antibody test : Cheap (<USD10/disposable shot) but for later stage. Antibody is produced inside body only after weeks people get infected. Mainly used to know you were infected before.
  • PCR (thermal cycler) : Cheap (Sales price of NinjaPCR is USD499/piece) but bothering post-processes including electrophoresis and illuminator.
  • qPCR (Real Time PCR) : No need of post-process but expensive (Commercial one costs USD20K-200K). Mainly used for medical PCR testing now.
  • LAMP : Cheap (Parts price of NinjaLAMP is USD50/piece), fast and easy but not widely approved for medical diagnosis because it's latest technique. Hope it will be changed soon.

Why NinjaPCR

PCR can be done simply by changing temperature of plastic tubes reagents and samples in using heat elements like peltier, heater and fan. So there're already several kinds of open source PCR machines. But almost all of them (tell me if you know any exception) are not precise because they use thermistor value on heater or aluminium tube holder as the temperature of samples inside plastic tube. NinjaPCR is only one open source PCR machine with thermal simulation model.

Here's the result. Red line is output of our simulation and blue line is measured temperature inside tubes. NinjaPCR supports 16 PCR tubes (Single tube projects are not practical because they cannot compare results with poisitive/negative control). WiFi is also supported and you can use NinjaPCR with not only PC but iOS and Android. But this thermal simulation is most unique and important point we think because we failed some testing without this feature.

NinjaLAMP in Indonesia, New York, and more

This thermal simulation is imported into NinjaLAMP. LAMP is simpler than PCR and its parts price is only USD50. You can make your own NinjaLAMP by connecting Arduino, few resistors, MOSFET, heater to tube holder. We are sharing how to calibrate with any heaters and tube holders on GitHub.

NinjaLAMP is already manufactured in Indonesia by my friend Akbar, founder of LifePatch who is also a hacker and biologist. Just after he shared a paper about how to detect COVID-19 with LAMP method at the end of April, I started making Ninja LAMP and just a week later, it’s done! I shipped only core parts to him and he 3d printed these lovely pink enclosures. Ninja LAMP is really easy to extend and he added status LED.

Armen in Columbia University, New York made his own LAMP machine forked from Ninja LAMP adding LCD display. I heard that he successfully detected positive sample with it.

By COVID-19, so many papers are published by researchers but not all of them has access to required hardwares. Open...

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