Comparative genomic in situ hybridization analysis of four cell lines derived from SV40 large T antigen-induced primitive neuroectodermal tumors of the rat revealed non-recurrent chromosomal copy number changes and DNA amplifications at chromosomal bands 2q34, 4q43qter and 15q12qter in cell lines TZ102, TZ103 and TZ107, respectively. Semi-quantitative PCR and western blot analysis demonstrated amplification and over-expression of the rat N-ras proto-oncogene in TZ102. Furthermore, all cell lines displayed aneuploid cell populations and variable chromosome numbers as assessed by flow cytometry and cytogenetics. These findings suggest that DNA amplification as well as genomic instability may contribute to the pathogenesis of SV40 large T antigen-induced primitive neuroectodermal tumors of the rat.