Cancer Res Commun. 2026 Jan 16.
Plasma cell-free DNA (cfDNA) analysis holds potential to improve detection of naturally occurring cancer in dogs, which serve as both important model organisms for human cancer and companion animals. However, there is limited comparative data on characteristics of canine and human cfDNA. We characterized cfDNA fragmentation in 254 plasma samples from 54 healthy dogs and 54 dogs with naturally occurring sarcomas, and compared them to 35 samples of human cfDNA. Using electrophoresis, whole genome sequencing with both short and long reads, and multiplexed quantitative PCR, we assessed both fragment size distribution and fragment end sequences. We then trained a random forest classifier to distinguish healthy dogs from those with sarcomas based on cfDNA fragmentation features. Canine cfDNA fragment size distributions showed a striking deviation from humans, including a median of only 39% of fragments between 50-700 base pairs versus 84% in human samples. Fragment end nucleotides were more random in dogs than in humans at multiple size ranges. Similar to human cancer patients, dogs with sarcomas had detectable copy number changes and characteristically shorter cfDNA fragments relative to healthy dogs, enabling classification of cancer samples with 91% accuracy. Our results demonstrate key differences in cfDNA fragmentation between dogs and humans, and highlight the potential for comparative translational research to advance blood-based early cancer detection in both species.