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Comparative Analysis of Cell-Free DNA Fragmentation Patterns in Canines with Sarcoma and Tumor-Free Canines and
Patricia Filippsen Favaro1,2,3, Yinghua Wang4,5, Bradon R McDonald1,2,3
1Center for Precision Medicine, University of Wisconsin-Madison, Madison, Wisconsin.
Cancer Research Communications
|January 16, 2026
Summary
Canine cell-free DNA (cfDNA) fragmentation differs significantly from humans, but cfDNA analysis can still detect canine cancer with 91% accuracy. This comparative research advances blood-based cancer detection in both dogs and humans.
Area of Science:
- Comparative oncology
- Genomics
- Biomarker discovery
Background:
- Plasma cell-free DNA (cfDNA) analysis shows promise for early cancer detection in dogs, which are valuable models for human cancer research.
- Limited comparative data exists on canine versus human cfDNA characteristics.
- Understanding these differences is crucial for developing effective blood-based cancer diagnostics.
Purpose of the Study:
- To characterize cfDNA fragmentation in healthy dogs and dogs with naturally occurring sarcomas.
- To compare canine cfDNA fragmentation patterns with those of humans.
- To evaluate the utility of cfDNA features for canine cancer detection.
Main Methods:
- Analysis of 254 plasma samples from dogs (54 healthy, 54 with sarcomas) and 35 human cfDNA samples.
- Utilized electrophoresis, whole genome sequencing (short and long reads), and quantitative PCR.
- Trained a random forest classifier on cfDNA fragmentation features.
Main Results:
- Canine cfDNA exhibited distinct fragment size distributions compared to humans (median 39% vs. 84% in 50-700 bp range).
- Canine cfDNA fragment ends were more random than human cfDNA across multiple size ranges.
- Dogs with sarcomas showed shorter cfDNA fragments and detectable copy number changes, enabling 91% accurate cancer classification.
Conclusions:
- Significant differences exist in cfDNA fragmentation between dogs and humans.
- cfDNA fragmentation patterns can accurately distinguish canine cancer from healthy controls.
- Comparative translational research using cfDNA holds potential for advancing early cancer detection in both companion animals and humans.
