Feasibility and promise of circulating tumor DNA analysis in dogs with naturally-occurring sarcoma

Abstract

Comparative studies of naturally-occurring canine cancers have provided new insight into many areas of cancer research. The inclusion of pet dogs in the development and validation of circulating tumor DNA (ctDNA) diagnostics may be uniquely informative for human translation for many reasons, including: high incidence of certain spontaneous cancers, repeated access to blood and tumor from the same individuals during the course of disease progression, and molecular heterogeneity of naturally-occurring cancers in dogs. Here, we present a feasibility study of ctDNA analysis performed in 9 healthy dogs and 39 dogs with either benign or malignant splenic tumors (hemangiosarcoma) using shallow whole genome sequencing (sWGS) of cell-free DNA. To enable detection and quantification of ctDNA using sWGS, we adapted two informatic approaches and compared their performance for the canine genome. At presentation, mean ctDNA tumor fraction in dogs with malignant splenic tumors was 11.2%, significantly higher than dogs with benign lesions (3.2%; p 0.001), achieving an AUC of 0.84. ctDNA tumor fraction was 14.3% and 9.0% in dogs with metastatic and localized disease, respectively although this difference was not statistically significant (p 0.227). In paired analysis, ctDNA fraction decreased from 11.0% to 7.9% after resection of malignant tumors (p 0.047). Our results demonstrate that ctDNA analysis is feasible in dogs with hemangiosarcoma using a cost-effective approach such as sWGS. Future studies are underway to validate these findings, and further evaluate the role of ctDNA to assess burden of disease and treatment response during drug development.

Horizons in Veterinary Precision Oncology: Fundamentals of Cancer Genomics and Applications of Liquid Biopsy for the Detection, Characterization, and Management of Cancer in Dogs

“…Published research on canine cfDNA has covered a variety of clinical applications, including trauma, sepsis, thromboembolism, and neoplasia, and has focused primarily on determining the concentration of cfDNA in plasma as correlated to a particular clinical state or as a predictor for certain clinical outcomes (84, 148-151, 167, 169, 191-203). Studies that evaluated cfDNA concentrations in healthy canine subjects have reported median concentrations ranging from less than 1 ng/mL to greater than 500 ng/mL (148,149,167,169,(194)(195)(196)(197)(198)(199)(200)(201)(202)(203)-significantly wider than the range documented in healthy humans (typically 0-20 ng/mL) (204). These wide-ranging findings suggest that additional research employing wellcontrolled, large-scale studies is required to better understand the fundamental characteristics of cfDNA in dogs; they also point to the need for standardized, reproducible methods for blood collection, extraction, and measurement of canine cfDNA.…”