Copy Number Alterations in Canine Urothelial Carcinomas: The Impact of Tumour Purity

Molecular genetic approaches have become indispensable in veterinary medicine for early tumour detection, confirming histomorphological diagnoses, and non-invasive diagnosis using urine samples. In canine urothelial carcinoma (UC), molecular testing includes BRAFV595E mutation analysis and the identification of specific copy number alterations (CNAs). CNAs affect multiple genes simultaneously, leading to their overexpression or underexpression. Recurrent gene gains on canine chromosomes (CFA)13 and CFA36 and losses on CFA19 are highly prevalent in canine UCs. This study evaluates CNA test performance and the influence of tumour purity on CNA test results using 76 histologically confirmed UC tissue samples. The tumour region of each histopathological section was measured, and its proportion relative to the total tissue area was calculated. In total, 58/76 cases (76.3%) were CNA-positive, defined by a ratio greater than 1.23 for both CFA13/19 and CFA36/19. A total of 14/18 negative cases had a ratio > 1.23 for CFA13/19 or CFA36/19. The sensitivity of this CNA assay depends on the applied thresholds, with a tumour-to-total tissue ratio of ≥20% yielding positive CNA results in 84% of cases, rising to 89% at ≥40%. These findings indicate that <20% tumour content and a moderate to high proportion of copy number-neutral cells may be associated with reduced CNA detectability.