Research & Publications

Explore our published research, conference presentations, ongoing pilot studies, and curated literature on cfDNA diagnostics in veterinary medicine.

Manuscripts

Peer-reviewed publications from the DeepScan team

Circulating cell-free DNA as a canine health biomarker

Veterinary Science · 2025

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Conference Abstracts

Presented at ESVONC 2025

DeepScan Diagnostics; University of Helsinki; Karolinska Institutet

Introduction

Circulating cell free DNA (cfDNA) is a promising analyte for detecting pathological processes before the clinical signs of a disease appear. However, cfDNA is a relatively unstable macromolecule and many preanalytical factors can affect its concentration. In this study, our findings outline the most important preanalytical factors and their effects on canine cfDNA testing from blood.

Materials and Methods

Over 3,000 dogs were recruited to this study with informed owner consent. Blood samples were collected from healthy dogs and dogs diagnosed with a variety of clinical diagnoses. Multiple conditions were tested for sample collection, transport, and reception steps. Different blood tube types, plasma separation protocols using centrifugation, cfDNA extraction methods, and DNA QC approaches were compared, and the best approaches were combined into a laboratory workflow.

Results

The most critical factors affecting the plasma cfDNA quality and quantity were found to be the extent of haemolysis and WBC contamination. These were followed by storage and transport temperatures, and the tube type used in blood collection. In contrast, the presence of lipids was not found to have a significant effect. cfDNA yield was also relatively stable across different plasma separation protocols.

Conclusions

cfDNA has the potential to revolutionise the diagnosis and monitoring of many diseases, and it is essential to standardise preanalytical factors as much as possible to ensure high-quality results.

DeepScan Diagnostics; University of Helsinki; Karolinska Institutet

Introduction

Circulating cell free DNA (cfDNA) is a promising liquid biopsy analyte for detecting pathological processes before the onset of clinical signs of a disease including cancer. Our findings highlight the utility of cfDNA testing in measuring canine health and monitoring disease treatment success.

Materials and Methods

>3000 dogs (2,314 presumed healthy; 421 with cancer diagnosis; and 595 with non-cancer diagnosis) were recruited with informed owner consent. An in-house workflow was developed to measure cfDNA from 1 mL EDTA plasma reliably and reproducibly. Internal controls and breed-specific reference ranges were generated to improve the test performance further.

Results

cfDNA concentration correlated with the severity of the underlying pathological process, with highest values seen in systemic cancers. Inflammatory diseases and localised cancers, most notably mast cell tumours (MCT), were seen in the lower end of the spectrum. The effect of pathological processes on cfDNA concentration was cumulative. Serial testing was found to be especially valuable in distinguishing cancers from e.g. inflammatory or chronic diseases, and in monitoring treatment efficiency and detecting disease recurrence.

Conclusions

We have developed a fast, affordable, and minimally invasive cfDNA-based test to measure the overall health for all dog breeds. The test has wide usability across many cancers as well as chronic and inflammatory diseases, and can be used as part of a standard blood panel to detect a wide range of illnesses, or as a standalone test to monitor the success of ongoing treatments against a known illness.

Veterinary Faculty, University of Ljubljana, Slovenia; DeepScan Diagnostics, Helsinki, Finland; Institute of Oncology Ljubljana, Slovenia

Introduction

Electrochemotherapy (ECT) with interleukin-12 gene electrotransfer (IL-12 GET) has shown local and systemic effects in treating canine mast cell tumours (MCT). To predict and evaluate the treatment response noninvasively (without tissue biopsies), liquid biopsy, such as cell-free DNA (cfDNA) from the blood, presents a promising diagnostic strategy. Therefore, this study aimed to evaluate cfDNA values from the blood of dogs with MCT treated with ECT + IL-12 GET to correlate the results with treatment response.

Materials and Methods

The study included 15 dogs with MCT (FNAB or histology) treated with the ECT + IL-12 GET. Blood plasma was collected before and 8 weeks after the treatment, and the response was evaluated using RECIST criteria. Next, cfDNA was isolated from plasma, and its concentration and fragment size distribution were analyzed.

Results

The results of this study indicated that 12 dogs achieved objective responses: complete or partial response (CR, PR); 1 had stable disease (SD), and 2 had progressive disease (PD). Furthermore, 8 weeks after treatment, the mean cfDNA values for CR dogs were the lowest at 1.97 ng/μL, while PD dogs had the highest values at 43.65 ng/μL. The PR mean was 7.66 ng/μL, and SD had an average of 6.28 ng/μL.

Conclusions

The results of this study suggest that cfDNA could be a promising biomarker for tracking tumour progression, predicting treatment response, and guiding clinical decisions. However, these findings should be interpreted cautiously, as larger studies with diverse tumour types and longer follow-ups are needed to confirm the results.

Pilot Studies

Ongoing and completed clinical pilot studies exploring CFD® across a range of conditions

CFD vs cPLI in Acute Pancreatitis

A Pilot Study Assessing the Correlation Between Canine Pancreatic Lipase Immunoreactivity (cPLI) and a Novel CFD-Based Diagnostic Test in Dogs With Suspected Acute Pancreatitis in Primary Care Practice

CFD Monitoring for Phenobarbital-Induced Hepatotoxicity

A Pilot Study Evaluating CFD as a Biomarker of Hepatocellular Injury in Dogs Receiving Phenobarbital for Idiopathic Epilepsy

CFD vs CRP in Neoplasia

A Pilot Study Evaluating the Relationship Between a Novel CFD-Based Diagnostic Test and C-Reactive Protein (CRP) in Dogs Undergoing Chemotherapy for Neoplasia

CFD vs LOAD in Osteoarthritis

A Pilot Study Assessing the Relationship Between a Novel CFD-Based Diagnostic Test and the Liverpool Osteoarthritis in Dogs (LOAD) Questionnaire in Dogs With Suspected or Diagnosed Canine Osteoarthritis

CFD in Splenic Disease

A Pilot Study Evaluating CFD as a Biomarker to Differentiate Malignant Tumours From Benign Changes in Dogs With Ultrasonographic Splenic Abnormalities

CFD and Palliative Steroid Therapy in Lymphoma

A Pilot Study Evaluating Whether CFD Levels Decrease Following Palliative Corticosteroid Therapy in Dogs With Lymphoma

CFD Monitoring in Lymphoma Remission

A Pilot Study Evaluating Whether Serial CFD Measurements Can Act as an Early Indicator of Relapse in Dogs With Lymphoma in Remission Following CHOP Chemotherapy

CFD After Amputation for Osteosarcoma

A Pilot Study Evaluating Whether CFD Can Detect Residual/Metastatic Disease and Inform Prognosis in Dogs Following Limb Amputation for Osteosarcoma

IMHA Monitoring with CFD

A Pilot Study Evaluating Whether a Novel CFD-Based Diagnostic Test Detects Disease Activity Faster Than Packed Cell Volume (PCV) and C-Reactive Protein (CRP) in Dogs With Immune-Mediated Hemolytic Anemia

Curated Literature

Key external publications supporting the science behind cfDNA diagnostics

Validation of cfDNA testing in dogs

Key Findings

Researchers at the Broad Institute demonstrated that various sample parameters, such as dog breed and tube type, significantly affect cfDNA measurements. They also confirmed that cfDNA is highly responsive to changes in the animal's health.

Relevance

This study strengthens the case for using cfDNA testing in veterinary diagnostics, highlighting its responsiveness and the need for standardised sampling methods in clinical settings.

cfDNA analysis in 1,500 clinical canine cases

Key Findings

PetDX's analysis demonstrated that cfDNA can provide valuable diagnostic information in dogs. However, the chosen methodology was costly and required too much blood as starting material, highlighting the need for more economical approaches to make large-scale cfDNA analysis feasible.

Relevance

Confirms that cfDNA is a useful diagnostic tool in veterinary contexts, paving the way for more affordable and efficient cfDNA-based methods in animal health diagnostics.

Comparative analysis of cfDNA-based methods for cancer detection

Key Findings

A multi-institutional study led by GRAIL with participation from Mayo Clinic and Francis Crick Institute found that methylation sequencing outperformed other techniques, even when using bisulfite sequencing which reduces the original sample by 90%. Advances like enzymatic methylation sequencing and digital PCR were not included but are expected to yield even better results.

Relevance

Underscores the importance of methylation analysis in cfDNA diagnostics, validating its accuracy and setting a high standard for future veterinary applications in early disease detection.

Early cancer detection and treatment outcomes

Key Findings

Oncologists reviewed how early each cancer type is typically detected and what the prognosis is. They concluded that earlier cancer detection can significantly influence treatment efficiency and patient survival.

Relevance

Underscores the potential benefits of early detection, hinting at cfDNA's role in transforming veterinary diagnostics by enabling earlier interventions. A similar assessment is needed in dogs to identify cancers most benefiting from early detection.

cfDNA fragment mapping for inferring gene activity in cancers

Key Findings

This study validated the approach of using the genomic mapping of cfDNA fragments relative to known CpG islands to identify genes that are activated or silenced in cancers.

Relevance

Supports cfDNA's capability to identify cancer-specific gene regulation patterns, emphasising its diagnostic potential for both human and veterinary oncology.

Post-treatment imaging vs. survival outcomes

Key Findings

A systematic review found no reliable link between imaging results after cancer treatment and patient survival, suggesting that traditional imaging may not be a dependable prognostic tool.

Relevance

Underlines the potential benefit of cfDNA as a prognostic marker, advocating for its integration into diagnostic protocols to provide more accurate prediction of outcomes compared to conventional imaging methods.

cfDNA-based cancer detection using digital PCR

Key Findings

Two Danish studies demonstrated that cfDNA analysis through digital PCR (dPCR) provides more accurate prognostic data compared to imaging. This method enhances the guidance of treatment choices by offering more reliable insights into cancer progression. A larger study (RECIST) is currently underway to further validate these findings.

Relevance

Reinforces cfDNA's role in improving cancer prognosis and personalised treatment, suggesting similar applications could significantly benefit veterinary diagnostics by offering more precise data than traditional methods.

Downloads & Printables

Clinical guides and educational materials for veterinarians and pet owners

Clinical Guides

Practical guides for veterinarians on using the CFD® marker in clinical practice

Educational Materials

Educational resources for pet owners and veterinary professionals

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