With fastGEN, we hit the nail on the head

Dr. Rastislav Slavkovsky , a young talented scientist, currently works at the Laboratory of experimental Medicine at the Institute of Molecular and Translational Medicine, Faculty of Medicine, Palacky University in Olomouc.

According to the Pubmed database, since 2006, he?has published 20 papers, one of which was in the prestigious journal Nature Communications. After completing his master‘s degree in Genetics and Biochemistry of Microorganisms at the University of?Chemistry and Technology in Prague, he obtained his doctorate in Medical Biochemistry at the Faculty of Medicine in Hradec Králové, Charles University, defending his dissertation on Wound Healing with a?focus on diabetic defects.

Dr. Slavkovsky and his team are behind the creation of?the fastGEN technology , and we will be talking about it and his collaboration with the BioVendor Group https://bit.ly/4bpFyAn today.

Good morning Dr. Slavkovsky, thank you for taking the time for our interview. Can you tell us about the journey from your idea to the first fastGEN product?

The role of our institute is to provide diagnostics for the?university hospital, mainly in the area of solid tumors. And not only for it, we are also a regional referral laboratory. We often examined solid colorectal tumors and various adenocarcinomas.

The demands of oncologists gradually increased, and the existing methods were no longer sufficient for us. We were faced with a decision on how to proceed. We explored various directions, one of which was to create our own method. In the end, this proved to be the best path for us.

So, you developed a methodology, tested it and started thinking about its further use because it made the process significantly easier?

Yes, in grant projects, it’s not just about the outputs being articles, but very often it can also be a patent, technology, or procedure... And one of our outputs was this unique methodology. And we were not ashamed of?it.

We said to ourselves, ?If we use it, why couldn‘t someone else use it?“ We tried to reach out to various companies; some were interested, some less so. And then we came across you, who were the?most?interested.

Why did you eventually choose the BioVendor Group?

BioVendor was an ideal partner for us. Not only because of the distance, less than a hundred kilometers from Olomouc to Brno. You had a strong distribution network built, which we were looking for in our partner. You also had experience with molecular biology and had established a base and knowledge regarding NGS?sequencing.

We clicked on all aspects, including on a personal level. So, the decision was made.

Who named the new methodology? And why fastGEN?

The word ?fast“ probably speaks for itself – we tried to make something really fast. Because standard procedures for creating a sequencing library typically take two days, which is a lot of pipetting time in the laboratory. We wanted something faster. Now, four hours from the start of work, we can run the sequencer, I think that‘s really fast. And GEN means we want to explore genes, but it can also be understood as an abbreviation of the word ?generation,“ so fastGEN as fast generation.

The original name was fastRAS, which is also a kind of?pun. RAS is an abbreviation of my name. ??

But primarily, RAS is the designation of the RAS pathway genes (KRAS, NRAS, or BRAF). These were the ones we genotyped first and named the method after them. Unfortunately, the name fastRAS was not universal enough because we didn‘t want a specific gene name in it. To be honest, the impulse to change came during discussions with our institute‘s director, Associate Professor Hajdúch, who has the main credit.

If we wanted to personify fastGEN and compare it?to a superhero, who would it be? Last time we had GENOVESA and Petr Bro? compared it to Superman. ??

Of course, the connection with speed immediately comes to mind... A typical fast superhero is Flash. He is?all red and would probably best represent fastGEN .

Let‘s move on to the fastGEN products themselves, their development, and practical use. How does research and development currently work (what are the roles of UMTM and BioVendor Group)? How are new products created?

The decision on what will be developed on fastGEN happens at two levels that communicate with each other.

One is ours at UMTM, where we try to meet the demands of our clinicians – in most cases, this relates to a new available drug. We always ask ourselves – is it solvable with fastGEN , and if so, we proceed with development.

The second level is here at BioVendor, where your commercial department communicates with customers and knows their requirements. When market analysis confirms the need, we proceed with the development of a new product together with the MolDx team from BioVendor Research & Diagnostic Products https://bit.ly/45J6oSV .

Are there any improvement projects running in parallel?

Yes, we have ideas on how to improve the technology itself, and yes, we are also taking steps to enhance it. For example, to make it usable on more sequencers, to?process more samples, to make our technology more user-friendly for combining with other technologies at the customer‘s site, or to explore new possibilities for?input material.

We are currently finishing the development of a?methodology where we follow up on fastGEN and where the input material will be RNA.

Tell us a little about the involvement of students – in BioVendor Group we support the generation of young scientists and their involvement in practice.

According to the UMTM website, you are now mentoring one doctoral student, nine master‘s students, and five bachelor‘s students – what is their role in the research and development of?fastGEN?

Crucial, without students fastGEN might not even exist. Students are often our hands, sometimes our heads, and for me also my mirror. I express my thoughts more easily when I have a student next to me, and I can discuss my ideas with them, talk about what and how might be feasible, what could work, what we can try.

The third generation of fastGEN was created as part of the diploma thesis of student Lucie Kotková , whose topic was related to the development of the fastGEN RAS (Solid Cancer kit).

In the end, the will of the supervisor, who assigns topics related to practice, not just a topic for the sake of fulfilling study duties, is also important.

What is the experience with fastGEN products in practice?

We have been using fastGEN for almost nine years, the first validated test was in 2015.

We started with KRAS, NRAS, BRAF genes, gradually expanding the portfolio to EGFR, IDH1, IDH2, POLE, PIK3CA, and others.

An interesting fact is that we also developed a prototype test for determining the genotype of SARS-CoV-2 in positive patients during the COVID-19 epidemic.

I would like to touch on the topic of small vs. large NGS panels – could you mention the advantages and disadvantages you perceive?

If we define the small one as fastGEN and the large one as a panel of genes ranging from 40 to 600 genes. The clear advantage of the large ones is that they target a large number of genes, and thus we obtain a large amount of information, based on which we can make further decisions. With the size of the panel, however, come negatives. These are mainly higher financial demands, less robustness, and longer processing time. With a small panel, we obtain less information, but that information is clearly targeted, and we can make decisions very quickly and efficiently based on that information.

If I know what I want to ask and what answer I am looking for, I use a small panel, but if I don‘t know and want to decide based on the results, I use a large panel.

What would be an example of using a large panel in practice?

A typical situation is when an oncologist exhausts standard therapy options, then turns to a molecular biologist to try to characterize the tumor and find a target, so we can propose an alternative therapy for the patient at the molecular tumor board, based on?available drugs.

What do you see as the main barrier to the more common use of NGS in clinical diagnostics?

I consider the biggest barrier to be technical-practical – that is, we have a small sample, or the sample is of poor quality. And the test result is then unusable. Therefore, I see great potential in the NGS field in developing methods capable of detecting biomarkers from very small amounts and low-quality samples.

And here I think we hit the nail on the head by not targeting a large number of genes but being able to?use?small samples with lower quality.

What would you say is the awareness and knowledge of NGS technology in the Czech Republic? And how do we compare to the world in this regard?

Personally, I think that knowledge of NGS technology is at a high level in the Czech Republic. There are many NGS experts here. We also have many sequencers. There are also various companies on the market that design solutions for NGS sequencing library preparation and deal with bioinformatics in the NGS field.

And as for fastGEN – I think it is gradually making its way into laboratories, and they have good experiences with it because it is very robust. People who work with it practically praise it because it is not demanding on?pipetting and prone to errors.

How do you see the future?

I would like fastGEN to be used in as many laboratories as possible in the future and for customers worldwide to be satisfied with it.

As for the future of NGS, I see it staying with us for a long time because the genetic information in us is the most important thing that makes us, and knowing what makes us is the basis of everything.

Finally, I have three bonus quick questions for you!

Basic and applied research – what do you enjoy about it?

In applied research, it is the satisfaction of the user; in?basic research, it is the desire to discover something that no one has known before.

Your greatest achievement so far?

Primarily my two children, a good relationship with my dear other half, and also fastGEN, which is my third child.

How do you relax?

In solitude in our forest, I cut down a tree, chop it into wood, and when it dries, I burn it in the fireplace with a?cup of tea and warm myself.

Thank you for your time and your answers!