Genome aberrations in canine mammary carcinomas and their detection in cell-free plasma DNA

Massive parallel sequencing (MPS) was performed in comparison to the respective somatic genome of each animal. Copy number and structural aberrations were validated using digital droplet PCR (ddPCR). Using mate-pair sequencing chromosomal aneuploidies were found in two tumors, frequent smaller deletions were found in one, inter-chromosomal fusions in one other, whereas one tumor was almost normal. These aberrations affect several known cancer associated genes such as cMYC and KIT. One common deletion of the proximal end of CFA27, harboring the tumor suppressor gene PFDN5 was detected in four tumors. Paired-end sequencing was conducted for 2 tumors (49 and 47), the 2 corresponding cell-free plasma DNA and PBMC specimen. High amplifications detected in the tumor are also visible in the animal’s plasma cfDNA.