At Miami University in Oxford, Ohio, genomics lives outside the lecture hall. It’s active, hands-on, and fully integrated into how students learn and how research gets done. At the core of its genomics efforts is Dr. Andor Kiss, director of the Center for Bioinformatics and Functional Genomics.
This past March, the center celebrated a major milestone: the installation of their Vega system, Miami’s first HiFi sequencing platform. Now, long-read data is being generated directly on campus, and students are stepping into roles that mirror real-world research settings. They’re prepping samples, running workflows, and making sense of complex results.
Projects that had been shelved due to budget or complexity are back in motion, with new ideas gaining traction across departments.
In our latest interview, Dr. Kiss shares how this new setup is helping move things forward both in the lab and the way science gets taught.
Q: Tell us about Miami University of Ohio and your role at the Center for Bioinformatics and Functional Genomics.
Dr. Andor Kiss: I’m the director of the Center for Bioinformatics and Functional Genomics, which is our genomics core at Miami University located in Oxford, OH. We have about 60 Principal Investigators (PIs) that use the facility and all of their associated graduate students and undergraduates. One of the things that’s really unique about our center is that we’re a training center, so we fully train all the users on the instrumentation and eventually allow them to use the instruments at will, with only having to pay for the consumables.
Being an open-door facility is a very unique model – Miami University is in that sweet spot of being big enough to have the capacity to house this kind of facility, but also small enough to allow people to walk through the door. Many people coming from bigger universities are really shocked at the level of quality of the facilities.
We also have a really robust undergraduate program. Seventy-five to eighty percent of our undergraduates have had a research undergraduate experience, which is pretty astonishing. That means that they are working in a PI’s lab and are usually paired with a graduate student, so we have quite a bit of independent research projects that are done by undergraduates. Graduate students also have 24-hour access to the facility and are able to use the instrumentation after hours, so it’s a very active facility. We also have classes from the local high schools that use the facility, so we service many groups of people and types of research, from biomedical work to a microbial study of frozen Antarctic lakes.
Q: What is the training process for the facility like?
I like to meet with each new student and their PI to talk about the arc of the project and where they’d like it to end up. Then as they move through their project, I train the students in each piece of instrumentation along the way, as opposed to trying to train them on five pieces of complex instrumentation in the first week.
Generally, I have a very hands-on approach walking them through the process for the first time and answering their questions along the way. Following that, I will let them handle the process and I won’t step in unless they’re about to make a significant mistake. After a few more training runs, I’ll let the students conduct their work during business hours when we are there to support, and from there if they are getting good results, we let them do their work at will.
So it’s an intensive process at the beginning, and then I essentially wean them off of support so that they gain the confidence to do it on their own. And this has been very effective because we’re able to have one-on-one training and the students so quickly gain a connection to how the process works.
Q: What barriers did you have to overcome to bring HiFi sequencing in house?
I really did want a PacBio instrument for a long time, but it had been just outside of our price point at Miami, because not being a part of a medical school, we don’t do large amounts of clinical testing.
So when the Vega system was introduced, it was not only at the ideal price point, but it was also the ideal physical size and infrastructure requirements because it just sits on the bench and plugs into 15-Amp service.
Q: What are some of the advantages you see to the Vega system?
It’s a completely unique technology, very easy to use, and is absolutely perfect for a genomics core of our size. We can’t make efficient use of a high-throughput instrument, so the Vega provides exactly the throughput we can use and support. The per run cost of the Vega is also cheaper than that of the Illumina MiSeq, so this has excited a lot of people on campus because it’s very well within the kind of usage-case scenarios that a lot of people have funding for.
Vega is a perfect teaching tool as well. It’s going to be integrated into at least two or three of our courses this fall, where undergraduates at both the junior and senior level will be making sequencing libraries, running the sequencing, and performing the bioinformatics. So this is really exciting, both for the students, who will be gaining a comprehensive skillset with this cutting-edge technology and for the instructors, who will be able to use this experience to generate pilot data for grants.
Q: What do you think is a misconception people have about long-read sequencing?
A lot of people have the misconception that it’s complex. Next-gen sequencing library generation many years ago, was complex, but with the ease of the PacBio kits nowadays, we’re seeing that the workflow is relatively straightforward and easy for almost anyone to pick up.
“During our PacBio training for the Vega, we had several students who had no previous experience in next-gen sequencing, but were able to perform the full workflow from beginning to end, no problem. A lot of people were quite shocked how simple it was because they expected it to be difficult. So the overwhelming response was ‘Wow, that was much easier than I thought it would be.”
There are some instruments that only a few highly-trained individuals can operate and with HiFi sequencing, that’s not the case. It really has become quite accessible to the “non-expert.”
Q: How do you think PacBio analysis is different from other NGS technologies?
We use the instrument through SMRT Link Cloud, and it works really well. I really like the fact that most, if not all, of PacBio analysis tools are available on GitHub and are open source. They are really well-documented and very straightforward to run. We run each analysis as independent Python scripts, which is well within the capacity of our students, because many of them are using R for a lot of their analyses already.
We’re seeing bioinformatics as not only straightforward, but also as an excellent teaching tool. One of the foci of Miami’s development with our McVey Data Science program is dealing with big datasets and making them understandable and interpretable. So working with sequencing data aligns perfectly with this mission because sequencing data is only getting bigger and bigger, and using Vega as a teaching instrument allows the students to actually acquire large datasets, process them, and make biological sense of them.
It’s also great to see so much innovation around data processing. For example, the fact that Fiber-seq only came out a couple of years ago you can now mark nucleosome positioning and acquire all the other data is pretty exciting.
Q: What are the applications you are looking forward to doing with HiFi sequencing?
We have so many foundational questions of biological function that can be answered with complete, long-read genome assemblies. I think PacBio has the best platform to do this and provides methyl sequencing at the same time. This, combined with the realization that many different splice variants can come from one particular gene, as well as the ability to examine this from a single-cell perspective, opens up a whole new world of epigenomics and transcriptomics that can only be done on the PacBio workflow.
“And now, with the introduction of Fiber-seq to characterize nucleosome positioning, the ability to tackle these applications with Vega is a game changer, especially for some of the bigger questions we haven’t yet been able to address –– like how does neuronal development work? How is the immune system triggered in response to certain stimuli? How is regeneration controlled? These are all things we can explore with Vega.”
Q: What are the first few projects you’re planning to conduct with your Vega system?
One of the big projects we’re doing with an advanced undergraduate/graduate class in the fall is to look at the epigenetic effects of cardiac stress in mice models. We know from earlier work with a collaborator how mice respond physiologically, but now we’ll have students doing the sequencing and bioinformatics of cardiac tissue from cold-stressed mice to determine how they respond genomically and epigenomically. We also expect this to generate pilot data for a grant proposal as well.
We also have a group looking to do metagenomics from complex samples that they’ve been unable to sequence with short reads. I think HiFi sequencing will provide the solution for them, so they are really excited about doing this on the Vega system.
Another group studies regeneration in newts and chickens and they’re planning to use the Vega for nucleosome positioning and methyl sequencing for that project. They’re pretty excited about that because previously there’s been a bit of a barrier for methyl sequencing with bisulfite conversion, so having a single, streamlined workflow is really appealing to them.
Some of these projects involve genomes that are up to 12 Gb and with large repeat sequences, which could be a losing battle for a short-read sequencer. So, a long-read approach with the Vega system will be a big advantage in these respects.
Q: What went into your decision when choosing between bringing an instrument in house or working with other service providers?
We’re a small core facility and we can’t duplicate our instrumentation, so there’s a number of factors that go into choosing an instrument: 1) how easy is it to use, 2) how much it costs, and 3) whether it fits into a unique niche filled by no other technology we currently have in the core. And that’s exactly where the Vega sits, allowing us to look at genomes, transcriptomes, and epigenomes in a single instrument.
The cost of the Vega is much lower for us than sending our samples to an outside facility, because there we’d have to pay for a service charge on top of the actual cost of sequencing. Having the ability to sequence in-house means that we don’t pay extra surcharges or for technician time, because the students are being trained to do it themselves.
I think having Vega will now allow everyone at the university do all these projects previously dismissed as too complicated, or too expensive, that now we’re able to do right on campus.
Frederick Sanger who invented Sanger sequencing said that every time there is a significant jump in technology, a whole new door of science opens up. And I think with the accessibility and the low cost of the Vega, that’s exactly where we are now – with the door wide open to a whole universe of things we’ve been waiting to explore.
Ready to see how Vega can transform your field?
Talk to a PacBio expert today.