Activities funded with the Women TechEU grant in this program :
• Setup the automated platform :
The Magelia of Inorevia is a microfluidic platform, designed to automate molecular biology protocols, improved their performance, and save up to 40 folds on reagents costs. The closed system it prevents from sample contamination. During the setup of the Magelia, the following activities have been performed:
o Protocol implementation strategy: Floating Genes’ protocol have been broken down, and each step has been prioritized in discussion with the team of Inorevia. It was decided to implement the first two PCR of the protocol, as they are the most standardized steps so far. The ligation and purification that follow these two PCR are currently being implemented.
o Test of microfluidics behaviors of Floating Genes’ reagents (viscosity, merging of droplets…). Samples of reagents were prepared and tested by Inorevia. This step allowed a good fidelity between the
o Installation of the machine and training of the team: the team of Inorevia came to install and calibrate the machine in Floating Genes’ laboratory. This point is crucial, as the machine runs on microfluidics, needs to be calibrated if it is moved. The team of Floating Genes was trained to use the Magelia. Specific attention is required in the sealing of plates, as well as setting up reagents and samples in the machine.
• Test cfDNA reference samples
The objective of this step is to test samples that are closer to clinical samples, than the synthetic samples. For that purpose, we created samples using human genomic DNA purchased from Promega, and digested with an endonuclease to mimic the fragmentation pattern of cell free DNA. We then added synthetic mutant DNA in the mixture in different Variant Allele Frenquencies (VAFs) and tested the protocol as if they were clinical samples.
Here we have shown that the Magelia delivers the expected results in line with the ones obtained until now manually. The Magelia improved the results at low VAF. More data are required to confirm these results.
• Evaluate the performance of the automated protocol vs. the manual implementation
The full protocol has been automated in two steps. The first 2 PCRs were implemented alone, and have shown superior performance. Then the full protocol has been implemented and tested, and improvement are required to tackle false positive resutls.
Comparison between the automated workflow and the manual workflow
The automated workflow has shown the following gains:
• 7 times faster than the manual workflow
• 40% more expensive per sample
• higher sensitivity at 0.06% mutant allele frequency (to be further confirmed)
• comparable erros rates on controls
Business model calibration: the economic comparison revealed that Enhance-seq automated in the Magelia is more expensive than the manual protocol, mostly because of the price of Inorevia’s cartridges. This price is based on a small purchased quantity. By purchasing larger amounts, the price of Inorevia’s cartridges may become competitive. Nevertheless, the gain in reproducibility will make the solution safer and more robust. Indeed the procedures to run the protocol are simpler, and any error can be traced back in the machine logs.
Achievements:
• The critical parts of the protocol of Floating Genes has successfully been translated into the Magelia so far. Further work is in process to make the full protocol automated and reliable on the Magelia.
• Tests on synthetic samples and cfDNA samples have been carried out, and are conclusive on the automated part of the protocol
• The comparison with the manual workflow of the automated part so far shows interesting gains, to be further confirmed.
