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The small number of cases means there are limited resources to investigate disease pathogenesis. This report describes a method of generating primary cell lines from freshly isolated human penile tissue using a clonal expansion approach on mitotically inactivated fibroblasts. Matched normal and penile cancer cell lines from two patients were generated and characterised. Molecular karyotyping and targeted sequencing were performed to compare their genomic landscape. Gains in 8q13.3, 10q23.2, 10q25.1, 10q26.13,12p13.33, 20q13.33, Xq21.1 or losses in Yq11.23 were consistent in both tumour cell lines. Gains in 8q13.3 and Xq21.1 cytobands positively correlated with changes in the expression of nearby genes. The top 20 differentially expressed genes are involved in immune responses like interferon alpha\/beta signalling. Additionally, there was an increase in integrin \u03b21, transglutaminase 1, keratins 5, 10, 14 and 16, and a decrease in involucrin protein expression. 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