How a University of Edinburgh spin-out uses the Element Biosciences AVITI System to detect tumor DNA in canine blood samples with higher confidence and a lower cost per sample.
Organization: CanCan Diagnostics, a University of Edinburgh spin-out founded in 2022
Application: Canine and feline cancer liquid biopsy for minimal residual disease (MRD) monitoring, plus tumor mutation profiling to guide targeted therapy
Platform: Element Biosciences AVITI System, adopted after comparing it with the team’s existing platform
Results: Slightly higher depth of coverage from low-input canine samples, fewer likely spurious low-fraction variant calls, and lower sequencing costs that allowed more cost-effective pricing on several tests
CanCan Diagnostics has a challenging problem to solve. The company, a University of Edinburgh spin-out founded in 2022, builds veterinary liquid biopsy tests that detect circulating tumor DNA in a dog’s and cat’s blood. The signal is faint, the background is noisy, and the amount of material you get from a canine sample is almost always small. Any sequencing platform that wants a place in that workflow has to prove it can pull a very small needle out of a very large haystack.
That was the bar Dr. Maciej Parys, CanCan’s founder and CEO, set when he first ran a sample on the AVITI System. AVITI cleared it, and CanCan has been building on the platform ever since.
CanCan runs two complementary assays to characterize cancers in dogs. One profiles a tumor’s mutations and points to the targeted therapies most likely to help. The second follow-on assay, and their highest volume test, is liquid biopsy for minimal residual disease (MRD), which tells a veterinarian whether a treated cancer is truly gone or quietly on its way back. CanCan’s tests go to veterinary oncologists in the UK, Europe, Hong Kong, China, Canada, the US, Brazil, and India, most of whom have never had a tool like this for their patients.
CanCan first became acquainted with Element sequencing data via the University of Edinburgh Genetics Core, which had brought an AVITI online. Parys had been watching the platform for a while and wanted to see how it compared with the Illumina workflow his team was already running. The question was simple: would the data hold up, and would it match what the team was used to?
The data held up, and then some. “It does, or it even looks better,” Parys said. “We got slightly enhanced depth of coverage, which was important for us because the input for dog samples is always relatively low.”
For CanCan, that extra depth was not a nice-to-have. A canine liquid biopsy for MRD starts from a blood draw that yields much less cell-free DNA (cfDNA) compared to humans, so every bit of sequencing coverage the team can pull from that material matters. CanCan moved its sequencing onto AVITI and has run on it since.
MRD testing depends on low variant allele frequency calling: finding a small fraction of tumor-derived DNA molecules in a haystack of DNA shed from normal cells, at concentrations that vary significantly from sample to sample. Parys found that AVITI’s higher base quality, a feature of Avidite Base Chemistry™, gave his team more confidence that low-fraction variant calls were true. In oncology panels, accuracy is one factor in determining the limit of detection (LOD), where real signal can become obscured by sequencing noise.
Veterinary oncology runs on a different economic model than human medicine. In most countries there is little or no pet insurance, so the owner pays directly. Price shapes how often a test gets used, putting cost of goods close to the center of the clinical decision.
Because AVITI lowered CanCan’s sequencing costs, the company is able to pass the savings along, introducing more cost-effective pricing on several tests, including tumor sequencing, without giving anything up on quality.
For Parys, the combination of cost and accuracy settled the decision. “If we can sequence everything much more cost-effectively and with higher precision, that makes a huge difference,” he said. “It benefits the patients, and it benefits us because we are more sure about the results. It was a no-brainer to go for it.”
Speed is also critical to CanCan’s mission. Today, a veterinarian collects the blood sample into a stabilizer tube, ships it to CanCan, and gets a result in about two weeks. The team is pushing that toward one week, because dog and cat owners are used to same-day answers from their vet for other types of tests, and two weeks feels long to them.
Behind that result is an in-house bioinformatics team of three that builds and runs CanCan’s analysis pipeline and reference data. One team member even helped build a new canine reference genome, an important resource for calling low-fraction variants in a species whose reference data has historically been less complete than the human equivalent.
The clearest picture of what sequencing already changes comes from the cases that stump every other method. “There were dogs that could not be diagnosed even after cytology, fluid analysis, and histopathology, especially with fusions,” Parys said. “With sequencing, we could say this is definitely cancer, and most probably this type.”
That sensitivity cuts both ways, and Parys is candid about it. A test that can see cancer this early can also flag it before a pet becomes visibly ill. In human medicine, enrichment panels have caught cancers years ahead of symptoms, and CanCan has seen the same pattern in dogs. Rather than chase the broad screening market, where a high false-positive rate is hard to explain to a worried owner, the company has focused first on MRD monitoring and is currently developing a confirmatory test that cross-checks another method’s positive result.
Ask Parys what he would tell another lab weighing the platform, and the answer is refreshingly plain.
“Just go for it and try. You will see it works really well and gives reliable results. People are afraid of change, but it is very reliable, it does not break often, the data output is really good, and the support is really good too, which was sometimes harder with other companies.”
Dr. Maciej Parys, Founder and CEO, CanCan Diagnostics
That reliability is what is letting CanCan grow beyond a single site. Samples arrive in the UK today, but the company has lined up a partner in Poland that recently acquired an AVITI, and the US lab it works with runs an AVITI as well. As volume climbs, Parys expects to bring an instrument in house, most likely a higher-throughput one, so the operation can scale with demand.
CanCan set out to bring the oncology assays used to understand human cancers to the pets that need them. AVITI gave the team a way to do that with more confidence and a lower cost per sample, and that combination is what is carrying the work forward, into feline cancer, into new tests, and into labs well beyond Edinburgh.
If you are building or using a target capture workflow for cancer research applications and want to see what AVITI can do for it, check out our resource, “Getting started with AVITI24 for clinical research.”
CanCan Diagnostics is a veterinary company, spun out of the University of Edinburgh in 2022, that develops liquid biopsy tests for cancer in dogs and currently works on development of liquid biopsy test for cats and started commercializing the tumor sequencing test for cats. Its tests profile tumor mutations to guide targeted therapy and monitor minimal residual disease after treatment.
After comparing AVITI with its existing Illumina workflow, CanCan saw slightly higher depth of coverage from low-input canine samples, higher base quality, fewer likely spurious low-fraction variant calls, and lower sequencing costs.
Liquid biopsy for MRD looks for rare tumor DNA molecules among many normal ones, so per-base accuracy is a factor in how low frequency a variant can be called by reducing sequencing noise.
Veterinarians currently receive results about two weeks after sample collection, and CanCan is working to shorten that to about one week.