When it comes to microbial genomics, Dr. Ibrahim Bitar doesn’t back down from a challenge. As an Assistant Professor of Microbiology at Charles University in Prague, and CEO of Gene Omics, a growing sequencing service provider in the Czech Republic, Dr. Bitar is on a mission to make high-quality, affordable long-read sequencing accessible across Central Europe.
With a Vega system powering research in his academic lab and a Revio system enabling cutting-edge services at Gene Omics, Dr. Bitar is a true champion of innovation, bringing PacBio HiFi sequencing to some of the most difficult-to-sequence samples, while empowering researchers throughout the region with the tools to transform their science.
In this interview, we dive into his passion for technology, his motivation for founding Gene Omics, and his vision for a future where HiFi technology is the new standard in sequencing.
Q: What inspired you to build a genomics service company in the Czech Republic?
Dr. Ibrahim Bitar: I had the idea of building this core facility for quite some time. I’ve been working here in the Czech Republic for seven years and throughout that time I’ve been exposed to different sequencing technologies. One thing that particularly caught my attention is the technology driving PacBio, I found out that there’s a lot of people who are interested in this technology but without the means to do it. These were researchers who were sending samples quite a distance in order to access this technology, so I realized it would be a good idea to bring access to a platform here in the Czech Republic.
And now that we have these platforms, I’m getting requests from all over Eastern Europe to visit the facility and check out the system, so I’m learning how widespread the interest in the technology is.
Q: How does HiFi long-read technology align with your mission for science?
I really believe in the technology, and I can see the direct impact this kind of accuracy and power has for our customers. For example, we have a customer doing clinical research in neurogenetics and they were running up against a wall because conventional short-read methods were not able to provide answers for them, so they came to us. In the end, we were able to help solve two cases, for which the answers resulted in tangible improvements in quality of life.
Having personally worked on this analysis, it’s something you could feel the satisfaction in, knowing that this work actually can change people’s lives. This was a hope I had, in theory, in opening our genomic service company, and now I’m able to see it in practice.
Q: What is your driving motivation in providing HiFi long-read technology as a service provider?
My driving motivation is to make this level of quality sequencing available for all and at an affordable price.
I am very hands-on when it comes to customers’ projects because I want to empower them to achieve their goals. I want to make this sequencing technology available for them, and ultimately for everyone throughout the Czech Republic. For this reason, I’m invested in their success and this makes it not just a business transaction, but a collaboration.
Q: When did you first see the advantages of PacBio HiFi sequencing compared to other platforms?
I had always had a positive experience with PacBio data, but the turning point for me was moving from our Sequel machine to the Revio. To compare the data, I did some mapping of the reads to see the difference between the systems, and there was a huge difference in sequence identity. I also found that when comparing the same isolate sequenced on the different systems, their phylogenetic trees would look completely different, so I realized how much additional insight HiFi sequencing was bringing to even the earlier platforms. This also holds across technologies too when I compared Revio HiFi data to sequencing with Illumina on the NovaSeq and with ONT on the PromethION.
Q: How is the Vega system changing your workflows?
Previously, it wasn’t economically friendly for us to sequence all of our isolates in a project on the Sequel because we were using a hybrid-technology model for our projects: We would sequence the majority of our isolates on short reads, and would sequence only one or two runs on the Sequel to close the genomes as representative circular plasmids as the final step of analysis.
My main focus is on plasmids that are quite big, so with short reads, each plasmid would consist of 15 or 20 contigs. This would require designing 100 to 150 primers for PCR and Sanger sequencing, to try to close these gaps, taking sometimes six months to close a single plasmid.
And now with Vega –– we’re no longer sequencing with short reads at all. We are using only HiFi sequencing, and no longer needing all of this downstream work.
With our short-read workflow I was publishing six or seven papers per year, and now with Vega I’m publishing fifteen, because I’m able to skip months of struggling with data. And it has really improved the quality of the research as well, to have entire projects of complete chromosomes from the beginning.
Q: How does HiFi sequencing compare to short reads?
Short reads used to be great, but that doesn’t feel like the case anymore. Now, you have the option for high-quality long reads at nearly the same cost as short reads, especially when you consider the savings on downstream analysis to finish short reads.
At this stage, I think scientists have to switch to long reads, otherwise they will be coming late to the technology. Even in my work five years ago, I was using short reads as a screening tool, just to select which genomes I should sequence with long reads to get a better look at them.
Q: What are some misconceptions people have about HiFi long reads?
I think a big one is that people assume you need to have ultra-long DNA, which is not always easy to get with all samples. So I make sure customers know this is not the case, and I’ve gotten three or four customers because of this information only.
I don’t have any difficulty convincing customers to go with HiFi sequencing –– they already know that it’s the best technology out there.
Q: What motivated you to go with PacBio technology over other competitors?
Before coming to the Czech Republic, I had previously only worked with short reads. My boss at my new lab here was excited about ONT platforms, but we quickly encountered problems: the bioinformatics posed challenges for our systems and we were finding it difficult to get the level of support we needed.
At this time I was starting to hear of this amazing technology called PacBio, where each contig was a closed chromosome and a closed plasmid that can bypass months of work. We bought a Sequel, and I started playing around a bit with the protocols to see what I can do and it was amazing.
One of the most remarkable aspects of switching over to PacBio was working with very well-defined bioinformatics pipelines, which ONT does not have. For example, when working with a pseudogene, I prepared myself to have to map it manually myself, but for this kind of analysis PacBio has a pipeline. There is a pipeline on GitHub for everything being tested, and this is something you can’t find with ONT, where even the assembly is very problematic.
With ONT, just slight tweaks to the analysis can yield different assemblies from the same samples, and all of this troubleshooting has to be done by the customer on their own. For each analysis, you have to go to see what other people are trying, whereas PacBio has clear software solutions for every analysis. With PacBio, the customer has the support, the software, and the means to carry out their sequencing successfully.
Q: How is the Vega benchtop system making HiFi sequencing more accessible to genomic researchers in the Czech Republic?
Where the Revio requires an investment of money and lab space, having the benchtop Vega system at an accessible price point brings HiFi sequencing to research groups in-house without needing a core facility. So, I think this will change the game for a lot of genomics labs, not just in the Czech Republic, but for every lab that needs to be mindful of space and money.
Now that many Czech researchers know that HiFi technology is in the Czech Republic, they want to try it. We’re seeing this with a lot of plant researchers and with an increasing interest in human genetics, where I can see this becoming the standard of technology.
HiFi technology can just simply take your research to the next level.
Q: What would you say to microbial researchers like yourself who are thinking of making this transition to HiFi sequencing?
Now is your chance to make this transition to long reads with Vega. The data that I’m producing with Vega is brilliant –– it’s a lot of coverage and economically friendly. I’m not paying anything more than I was paying for short reads, and this is the way toward improving your research, it’s as simple as that. HiFi sequencing is the next big thing and if you don’t adopt this technology then in a year or two, max, you will be behind.
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