iGEM Patras 2021

Proposed Implementation

The knowledge is not power! The implementation of knowledge is power!

  • All
  • Overview
  • Oxford Nanopore MinION Implementation
  • Novel Variants Future Steps
  • Bioethics & Safety

Our vision for Project PGasus is to set the foundations and become an inspiration for future scientists to take this research a step further, aiming to detect not only common and rare variants but also novel ones. We seek this because, as it has already been clear, while many patients underwent pharmacogenomic testing before drug administration and dosing adjustment, according to EMA’s and FDA’s guidelines, they eventually experienced drug ineffectiveness and side effects. So, these unreported, low-frequency variants should be considered in determining drug dosage, considering their significant effects on a patient’s health.

Before starting, we had to be honest about the implementation of our project. PGasus is mainly a project that concerns basic research and has no direct application to society and all the specialties of scientists or doctors. However, there are a few ways that we envision our end users getting advantage of our project if the proper steps are taken.

Oxford Nanopore MinION Implementation

First of all, we have to consider diagnostic laboratories of either public or private clinics or companies as the primary end-users of our project. The comprehensive workflow for identifying PGx variants that our team proposes requires knowledge of NGS analysis results that a physician or a doctor cannot do. That was clear to us from the beginning. Of course, the second time we reached all the doctors we had contacted during our Human Practices - when our project was fully developed - they confirmed our initial thoughts. So, a typical private doctor in his office or a microbiologist in his/her laboratory not only could not analyze such results but also would find it hard at the beginning to operate the Oxford Nanopore NGS sequencer. However, the experts in Bioinformatics placed in diagnostics laboratories could easily analyze the results derived from the NGS device.

After spending some time with the Oxford Nanopore MinION, the members of our team have explored all the advantages that make it the perfect tool to sequence a patient’s genome. For starters, it is a one-of-a-kind technology that enables direct yet real-time analysis of short to ultra-long fragments of DNA or RNA in fully scalable formats. That makes it excellent for a potential targeted NGS analysis of the two genes like we did through our project. Also, its portability, accuracy, low cost, and time-saving analysis are the other four reasons a diagnostic center should prefer this device instead of any other heavier and far more expensive ones. At this point, we must mention that although our team has already discovered its potentials as a diagnostic tool, Oxford Nanopore MinION should be approved by the FDA and other health regulators as a legitimate device capable of diagnostic procedures, as Ms. Virginia Safra, an employee in the Department of Medical Devices if our National Organisation for Medicines, informed us.

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Despite that we have found the end-users of our project, we were worried that through it still, PGx cannot be accessible to everyone. So, we thought about how the scientific field we are dealing with could reach every person around the world and finally achieve the ideal personalized therapy. Of course, Oxford Nanopore MinION as a portable NGS device has the potential to serve this purpose. Firstly, MinION is a portable, pocket-sized sequencer weighing less than 450g, easily connected to a laptop with a USB. Its portability makes it ideal for purchase in remote areas and islands where doctors in clinics and hospitals do not have the space to host massive devices. Secondly, we have to mention that it is as accurate as other NGS sequencers. Thirdly, the fact that it is very cheap to not only purchase but also operate by an individual is a clear advantage. Lastly, the time needed to exact the NGS results is less than 48 hours, most of the time.

However, in our last words, we started referring to physicians purchasing it and individuals operating it. Since we said that Oxford Nanopore MinION could only be used effectively by diagnostics laboratories, how is this possible? The answer to that is developing a neural network for automatization of the NGS analysis to make the results understandable by health professionals. By this being the case, and only if we achieve this, the end-users can also be doctors, physicians, and microbiologists in private clinics and laboratories. In this way, we can make Pharmacogenomics more easily implemented in clinical practice and accessible to every patient.

Novel Variants Future Steps

Of course, after our discussion with Mr. Klimentidis and Mr. Vizirianakis, we realized that there are many steps to be made in order for the novel variants we detected to be approved and to adjust a drug’s dosage regarding their existence in a patient’s genes.

After detecting the novel variants and acquiring knowledge that some of them have damaging effects on the CYP2D6 and CYP2C19 enzymes' activity, after the functional characterization procedures we conducted, we propose that they should be included in research studies and clinical trials. This is a crucial step to be made; since then, we will be able to validate the exact dose that a patient with such variants should be administered. This is a long-lasting procedure because the different disorders in the patients' physiology, such as cardiopathies or nephropathies, must be considered, as Mr. Vizirianakis mentioned. Moreover, for once more, the Food and Drug Administration (FDA) must approve the clinical trials conducted upon these variants and the proper dosage administration of the drugs metabolized by the enzymes of interest, as Mr. Klimentidis informed us.

After the FDA approval, lab technicians in diagnostic labs, for starters and later doctors in clinics, will have the prospect to also consider these variants before prescribing a drug to a patient by adjusting its dose. We have to admit that even if it is a long-term procedure, it can lead to the enrichment of the already existing pharmacogenetic panels with new variants. Thus, the faster this process of improving the services provided by pharmacogenomic platforms occurs, the less likely it is that a patient will not have a proper dose adjustment due to a novel variant he may have in his genome.

So, this is a very crucial challenge for our team in the future years to be considered, which will not make Pharmacogenomics accessible to everyone - like the previous one - but make its implementation approved, better, and flueless over the years.

Bioethics & Safety

Concerning the safety aspects of Project PGasus, regarding its implementation, it is known that no apparent risks should be raised for each procedure.

For any procedure concerning the usage of blood or DNA sample for sequencing purposes, all the bioethical protocols must be followed. As a team, we believe that Ethics is an integral part of the fields of Science and Technology. There are many different factors to consider when trying to approach their ethical aspects, especially when attempting to do that for the newly emerged field of Synthetic Biology.

The issue of detailed information of the participants about the process and the content of the project and its future extensions is crucial for obtaining their valid consent. The informed consent of the participants in such projects is a condition, of course. For this reason, applying for approval of the program to the Ethics and Ethics Committee of the University and obtaining approval from it ensures that the legal procedures have been followed and all the prescribed conditions have been met. Moreover, the strict application of what is stated in the documents for approval of the study is a guarantee of the prevention of ethical issues. It should not be forgotten that research should be conducted with respect for human dignity, as protected by guidelines, international conventions, and declarations (such as the UNESCO Universal Declaration of Bioethics and Human Rights, the UN Convention on the Elimination of All Forms of Discrimination against Women). Finally, researchers must adhere to the professional ethics of their field when conducting research of that type.

The importance of the safety of personal data must also be pointed out. The General Regulation for Data Protection (EU) 2016/679 (GKPD), Law 4624/2019, and Law 2472/1997 apply, which has a participant's consent form after the thorough information and a format regarding the personal data collected, stored, and subject to processing. Moreover, it is noted that when a scientist uses DNA samples, it is crucial to state the reasons justifying the collection, storage, and processing of DNA samples. At the same time, pseudonymization and encryption of DNA samples are also required (article 22 et seq. Law 4624/2019). The keeping of a genetic data file must be notified to the Personal Data Protection Authority, and the general public's scaremongering is a crucial issue that should be mentioned.

In our team’s case, all ethical protocols have been approved by the Institutional Review Board of the University of Patras, and we complied with GDPR for data anonymity and data analysis. In order to keep in mind the exact bioethical issues, we prioritized coming in contact with the Laboratory of Medical Law & Bioethics in AUTh to inform us about the legal-ethical issues that may arise from a project like ours. As far as the scientific field we are dealing with is concerned, there is a widespread view that Pharmacogenomics is ambiguous because of DNA samples' need and storage. So, with the aforementioned laboratory's instructors, we tried to solve this problem through the Informed Patient Consent Form that must be provided to each participant, after referring to the necessary information upon our project and answering all of his/her questions.

For any experiments and wet lab procedures that must be conducted with the help of Oxford Nanopore MinION, the end-users have to be cautious by using this device to prevent unexpected and undesirable problems. For more information, you can reach our Safety page.