At the University of Michigan, two cores on opposite sides of campus are working together to change what’s possible in genomics. Judith Meyers helps run the Advanced Genomics Core (AGC), where her focus is making sure researchers have the tools and infrastructure they need to keep asking bigger questions. A few buildings away, Dr. Zachary Freeman directs the Transgenic Animal Model Core (TAMC), bringing his veterinary lens to the world of genome editing, where the difference between a clean edit and a failed model often comes down to accuracy.
On their own, each core plays an important role. But together, they’ve built a partnership that creates a pipeline where Meyers’ commitment to access meets Freeman’s demand for rigor. They’re showing how HiFi long-read sequencing allows them to move beyond traditional methods so that transgenic research and editing can evolve from trial-and-error to a reliable path toward accurate characterization of transgenic models.
Q: How do each of your cores function and rely on one another?
Judy: At the Advanced Genomics Core, we are committed to staying on the cutting edge of genomics and offering new exciting platforms and technologies. Since our initial start with DNA sequencing in the late nineties, we have expanded to RNA sequencing, single-cell sequencing, spatialomics, epigenomics, and beyond. We are a full-service laboratory, so users can come to us at any point in the process that they are comfortable with. That could mean starting with blocks of tissue where we will do the sectioning and staining, or labs that are more comfortable with library prep can provide us with client-made libraries for our “load-and-go” offering. We also have an educational component to our genomics core, where we partner with vendors, other core facilities, including our bioinformatics core, to run workshops.
Zach: At the Transgenic Animal Model Core, we produce transgenic animal models with consultation for CRISPR-Cas9 genome editing, transgenic, and gene targeting research.
Our goal is to provide end-to-end services around the development of new animal models, and also the management and characterization of existing models. Customers often come to us wanting to make a model of a human disease, so we use technologies like CRISPR-Cas9 to modify the genome in mice and rats so that they can then use them to conduct their research. CRISPR-Cas9 is not perfect, and often errors are introduced in the editing process and it can be difficult to detect whether the correct alleles are present.
We need to find the animals that are edited correctly with sensitive assays that can ensure we do not miss any animals that are correct. I realized that we needed long-read sequencing to accurately characterize these models, so we partnered with Judy and the Advanced Genomics Core. Our lab handles the CRISPR design, validation, and sample prep, and then we hand it off to Judy’s team to do the QC, library prep, and sequencing. Our bioinformaticist is also based in the AGC, so we work together to develop custom pipelines to correctly align our genomes to what we expect after genome editing.
Q: How has the technology in your cores evolved?
Zach: For our transgenic work, we had been using multiple PCRs with Sanger sequencing to confirm gene insertion, but this becomes difficult when we need to characterize a gene that is several thousand base pairs long. Oftentimes our lab staff would have to repeat a PCR three or four times and it gets very frustrating for them.
We initially started with other long-read technology to do CRISPR sequencing but could only run one sample per flow cell and not being able to scale made it too costly for us. Learning that we could multiplex 48 samples on a single SMRT Cell with PureTarget panels was the biggest draw of this technology for us because suddenly it became very cost effective for us. Instead of thousands of dollars to characterize one animal, with PureTarget we could do it for a couple hundred dollars and very much change how we were doing things.
PureTarget has also been powerful in characterizing these very long insertions. Where we used to have to run 3–4 PCRs, now we do one screening PCR, and then PureTarget, and we are done. So, we’ve been able to consolidate this process into one streamlined assay. Not only does PureTarget make the workflow easier, we also get a much better picture of what changes have been made and what is actually in the genome because we don’t have PCR introducing bias into the process.
Judy: Long-read sequencing technology in the AGC has evolved a lot over the years. When I joined in 2017, we had an early PacBio instrument, but couldn’t build a big enough business to support it. We brought in another long-read sequencing technology which has it’s own strengths, but the accuracy of HiFi sequencing was really one of the tipping points for us to return to PacBio technology with the Vega system.
HiFi read accuracy has been extremely valuable for those clients that want to assemble genomes, but have to get through difficult repetitive regions to do so. These clients need the accuracy of HiFi sequencing to map and align their genomes.
And as Zach mentioned, HiFi accuracy has been key to our work with the Transgenic Animal Model Core. Some of their animal models are made with random transgenesis where the genes integrate at a random location and we need to narrow down where they are. We were finding that he needed better accuracy to home in on those locations in the genome, so these were our very first samples that we ran on the Vega system. The quality of the reads and the Q scores combined with the length that we get with HiFi WGS allow us to accurately pinpoint these “lost” transgenes.
The long-read sequencing team at the Advanced Genomics Core
Q: What have been the reactions to these technology evolutions within your cores and where do you see them moving ahead?
Judy: After installing the Vega, we went from 0 to 100 very quickly, and suddenly we had a waiting line for HiFi sequencing. We’re very pleased with the uptick and our next step may be to move up to a Revio system to keep up with business, but certainly the benchtop, reasonably priced Vega has been a great thing for us to do the R&D work that we wanted to do and it performs beautifully. We have a great team of technicians in the lab driving the R&D work forward.
Zach: We had some initial reluctance from my lab to transition to a new technology, but we’re finding that we’re saving so much time and effort. We are discovering aspects of genome edits from the data that we simply couldn’t see before and now we all love it.
Long reads are just so much more powerful for so many applications and we are discovering many things in the long-read data that we never could see with Sanger or short reads. I’m constantly telling people about the benefits of switching to long reads because it changes your perspective on how you do gene editing. With this technology, we can now make models that are highly translationally relevant and can really improve the way that we’re making models to study disease and impact human medicine.
For both cores, adopting HiFi sequencing was an upgrade and a leap of trust built on collaboration and curiosity. The partnership between the AGC and TAMC has changed the questions we ask about genetic validation. Now, instead of asking “Can we find it?” we can ask, “How far can we go?”
Want to discover how far you can go with HiFi sequencing in your lab?
Learn more about the technologies driving University of Michigan’s success: HiFi gene editing, Vega platform, and PureTarget panels.