Engineering success

Crucial aspect of our project we succeed in is routine laboratory processes robotic automation.

Before establishing Genomus we have taken an attempt to run all the lab processes to find out our own genotypes. It took us about 5 hours to get results. We have come to the conclusion that we wouldn’t manage to provide the participants with precise results in time without automatic pipetting, DNA isolation and result analysis. After partial robotic automation the time consumption reduced up to 2.5 hours (from sampling to result available for comparison on Genomus website). Among other things, automation allows us to avoid employment of additional lab staff and manage everything on our own, which significantly reduces the cost of the project, allowing it to remain non-commercial despite the large number of participants and limited funding.

Now two types of robots, both from DNA-TECNOLOGY®, are ready to use in Pirogov Medical University laboratory: automated DNA extraction system and automated PCR mix preparation system. These are easy to use, robust bench-top instruments enabling us to run up to 728 qPCR reactions at the same time using DTprime Real-time Detection Thermal Cycler and other compatible equipment of the same brand.

An important challenge for us is development of custom automatic protocols for robots and improving the equipment compatibility to achieve full automation of Pirogov Medical University laboratory.

For this reason we enter into cooperation with engineers from DNA-TECHNOLOGY. This time our programmer works on automatic uploading of results from Thermal Cyclers to the website. We try to set up software for remote monitoring of all stages of the lab process as well.

With our cybersecurity specialist together, we develop a secure channel for personal data and GeneID exchange with participants beyond Pirogov Medical University to provide them access to the Genomus website and application for a smartphone, where a participant can get the analysis results and their interpretation and compare them with the results of another participant using a QR code. This is crucial for our project expansion.

Our next idea, which we didn't manage this year due to the pandemic and laboratory access restrictions for more than 6 months, is to create a portable genotyping system. We decided not to waste time, but to master methods of isothermal DNA amplification (RPA), crispr/Cas9 SNP detection. We read a lot about fluorescent reporter systems and microfluidics we could use to create engineering solutions that are simple and available for users far from biology and medicine. Our idea is to make preconception diagnostics as simple and accessible as a pregnancy test.

Collaborating with the SUNY ONEONTA team, we focused on their flappase based system for cow genotyping. More information about their system can be found here

One of our joint challenges is to create a reporter system with sufficient fluorescence for precise detection by a smartphone's camera using synthetic biology tools, or a fluorescence amplifier compatible with a portable genotyping system and a smartphone.

We study the projects of the teams that worked on fluorescent reporter systems in previous years and think about how we can use the available parts to create the system we need.

Among other things, we are thinking about integration of the portable detection software with our smartphone application and best design of a laboratory-on-a-chip, which we can manufacture at the Pirogov University's prototyping and microfluidics center after the restrictions end.