Safety is the priority. Quality is the standard.
- Laboratory Safety
In the 2018 iGEM competition, the TU Delft team established the phrase "safety always" in their project instead of the well-known "safety first." And they were right! A year later, at the 2019 iGEM competition, the Athens team provided us with the great motto of "Safety isn't expensive, it's priceless." This adage is one of the many that indicates the necessity of safety in scientific projects.
The aforementioned former teams helped us understand the importance of safety in the iGEM competition. But, to which "safety" are they referring? Although laboratory safety aspects are mainly included in this term, ethical issues also arise. All these vary from biosafety rules about the understudy organism and eco-friendly instructions to bioethical limits as far as responsible use is concerned.
For our team, safety plays an essential role in protecting ourselves and our lab colleagues, being aware of the possible risks, and handling them. As part of that, before starting the experiments, the wet lab team was trained by our Instructor, Stavroula Siamoglou, according to the biosafety rules while working on a Laboratory of Molecular Biology to handle risky situations adequately.
We aim to create a comprehensive workflow for the identification & functional characterization of Pharmacogenomics variants.
Novel and rare variants were detected using Next-Generation Sequencing and clinical data from patients with psychiatric disorders. In order to further validate the functional effect of such variants, site-directed mutagenesis in eukaryotic cells (293FT line) has been performed.
The 293FT Cell Line is a fast-growing, highly transfectable clonal isolate derived from human embryonic kidney cells transformed with the SV40 large T antigen, allowing very high levels of protein to be expressed from vectors containing the SV40 origin.
A portable NGS device (Oxford nanopore MinION) in a compact size to parallel sequence common, rare and novel variants was used. Whole pharmacogene sequencing with Oxford nanopore MinION was cost-saving and just as accurate as of the other NGS sequencers.
The first thing a user has to do is place the Oxford Nanopore Technologies device on a flat and stable surface and ensure any cables that are to be plugged into the Oxford Nanopore Technologies device are not stretched. Taut cables pose electrical and physical risks to the user. It is necessary to minimize contact with the chemicals by wearing protective clothing, safety glasses, and gloves and minimize inhalation of chemicals by using appropriate ventilation, checking continuously for any spills or leakages, and following the clean-up guidelines provided. All device components should be handled, stored, and disposed of by local, state/provincial, or national laws and regulations. According to the required safety regulations and rules, samples loaded into the flow cell should be used, stored, and disposed of. Samples containing infectious agents should be handled with the greatest of care and by the required safety regulations and laws. It is good laboratory practice to always wear safety glasses, gloves (2 pairs if working with infectious agents), and a lab coat.
Proof of legal and appropriate destruction of any contaminated flow cells will be required. The sequencing device shall be decontaminated before decommissioning. All local regulations for electronic and electrical waste shall be followed regarding disposal of the components if they are not returned to Oxford Nanopore Technologies. According to the local rules, the flow cell buffer, wash kit buffers, and sample preparation kit buffers must be disposed of. The used liquid product must not be disposed of through domestic water waste infrastructure (e.g., a sink). The flow cell buffer, the sample preparation kit, and wash kit buffers must not be mixed in ways other than those stated in the user protocols and must be kept away from strong acids and alkalis.
The functional range of electronics is within environmental temperatures of +5°C to +40°C. Also, the bottom of the instrument heats up during operation. Last but not least, customers are advised to use the 19 VDC power supply provided with the device. If a different power source is used, the power source must be safely isolated with a fuse or circuit breaker. In case of emergency, users have to switch off the oxford nanopore technologies device. At the mains power source and unplug the power cable from the device.
Furthermore, in our Dry-Lab space, no possible risk was identified and needed to be managed. Noteworthy, for these procedures and generally for this experiment, no apparent dangers have been raised. However, thanks to our instructor Diana-Hortensia, Portman, the safety and security for conducting our team's investigations was one of the most critical challenges in our iGEM journey. The Institutional Review Board has also approved all the University of Patras ethical protocols and we complied with GDPR for data anonymity and data analysis.
For more information and details, you can visit our Safety Form!
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 we attempt to do that for the newly emerged field of Synthetic Biology. While searching the scientific literature, we realized various definitions of Synthetic Biology, but not entirely adequate. One that could partially be satisfactory is that Synthetic Biology is more than just another field in Biology or Engineering. It's a fusion of these two in ways that can help you design and build entirely new systems or copy the already existing ones artificially.
In order to keep in mind the exact bioethical issues, we prioritize coming in contact with the Laboratory of Medical Law & Bioethics AUTh to inform us about the legal-ethical issues that may arise from a project like ours.
The laboratory instructors said that the issue of detailed information of the participants about the process and the content of the project, as well as 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 application 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). UNESCO Declaration on the Human Genome) but also the Constitution of Greece and other national legislative texts. Finally, researchers must adhere to the professional ethics of their field when conducting research.
Furthermore, they pointed out the importance of the safety of personal data. At the same time, they mentioned 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.
Below you can find our consent form legally approved from the Committee of Ethics in Research of the University of Patras both in Greek and English.
It is also noted that, when we use 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.
Overall, there is a widespread view that pharmacogenomics is an ambiguous subject because of DNA samples' need and storage. So, 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. People should realize that Synthetic Biology and Pharmacogenomics can help solve societal issues using logical arguments. We should not be afraid of contrasting opinions since they can result in fruitful discussions.