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.
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 source hardware is a key to catch up their urgent needs. If you are a member of local hackerspaces, you may already help health care workers by making PPE like facegurds. but maybe we, makers can do something more.
Who needs Ninja LAMP and Ninja qPCR?
Look at the long lines at test sites. Sometimes they have to wait 5 or more days to get results. If health care workers can use enough machines, required days will be shorten drastically.
Look at the Akbar’s Indonesia. Almost 300 million people lives in more than 10K islands. Total confirmed number of COVID-19 patients exceeded 162K on Aug28 and situation is getting worse. Imagine if every small hospitals in such islands have their own qPCR machines. Imagine how many lives can be saved? What’s in need is not a single 200K dollar machine in capital city, but USD50 machines in 4K islands.
Not only islands, closed, separated or isolated areas can be found everywhere in the world. Cruise ships, Refugee camps, Aircrafts, Offices, Classrooms. Imagine if all of them have their own qPCR machines.
After COVID-19, we need to change a lot. But if there’s only pricy machines in market, some extraordinary ideas will be rejected easily due to its cost. For example, how about giving one qPCR machine to all PCR-testing license holders?
In case of Japan, it takes at least 3 years to acquire license to become a health care worker who is allowed to pick samples from patients for diagnosis. Establishment of new medical license for test site workers that can be acquired in shorter term is another example of preparation we can do for 2nd wave.
PCR is essential method not only for diagnosis but also for citizen science and education. If we can use affordable qPCR machines at home, it changes our daily lives. Small kids with food allergy can check their foods by themselves with their phones. Most of us including me has never had DNA experiments in school because we don’t have PCR machine in classroom.
We're making Ninja qPCR with people all over the world
We started Ninja qPCR project form March. Since that, so many people joined our project. BioClub, biohackerspace in Tokyo host an event for networking. individuals help us with their knowledges and donations. Company in China and Japan helps us to make metal parts and custom heater at lowest price. That could never be happend if Ninja qPCR is closed source project. That’s exactly the power of open source movement.
I (Shingo) and Mariko are both software engineers. We managed to learn how to make hardware but no background about biology at all. Thanks to all people in this map, Ninja qPCR project goes much faster than we have expected first. We stayed at home for 2.5 months rising 2 kids. Japan is still in the midst of COVID-19 2nd wave but we feel that we're connected to the world.
At first, we tested optical filter with lego, baby food bottle and bath salt with fluorescence. It looks like toy but its wavelength is exactly the same to qPCR reagents so we’re serious. Now, optical engineer Ashim is helping us from Kathmandu.
MISUMI, largest tool distributer in Japan donated tube holder. Chinese company in Guangdong, China also donated us tube holder and custom heater. They help us when we manufacture Ninja qPCR.
Currently designing circuit following this diagram. We're shrinking parts cost and expanding elasticity. You can change number of tubes depending on budget.
Latest 3D model of Ninja qPCR is shared and updated at Autodesk Gallery.
Software is written from scratch with Vue.js and NumPy. Of course Ninja qPCR supports WiFi. PC, iOS and Android can use it.
All software and hardware for PCR, WiFi settings and basic user interface required for first test are already finished. After adding optical control within months, we will run safe COVID-19 PCR testing with synthetic gene that contains unique sequence of virus.
What we need
We still need many kinds of help. Fund to manufacture in China. Feedbacks from commercial qPCR users to improve UI. Connection with FDA consultants is also needed because commercial model with US FDA license is needed for medical diagnosis. Making hardware is hard. Donation via PayPal is always welcomed. You can contact me anytime by Facebook Messenger or email.