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The diagnostic differentiation between canine fibrosarcomas and peripheral nerve sheath tumours (PNSTs) is based on histopathological phenotype. Histological differentiation of these tumours can, however, be challenging and there is a lack of immunohistochemical markers to prove their histogenic origin. To identify possible PNST markers and to further characterize their histogenic origin we compared histologically well-defined canine fibrosarcomas and PNSTs by cDNA microarray analysis. Forty-five annotated gene products were significantly differentially expressed between both tumour types. Seven of these gene products, known to be specifically expressed in neuroectodermal tissues, had higher expression levels in PNSTs: FMN2, KIF1B, GLI1, ROBO1, NMUR2, DOK4 and HMG20B. Conversely, eight genes associated with carcinogenesis had higher expression in fibrosarcomas: FHL2, PLAGL1, FNBP1L, BAG2, HK1, CSK and Cox5A. Comparison of the fibrosarcoma and PNST transcriptome therefore identified PNST phenotype-associated genes involved in neuroectodermal differentiation, which may be useful as diagnostic markers. Furthermore, the genes associated with the fibrosarcoma phenotype may serve as markers to differentiate fibrosarcomas from other tumour types.