Malignant peripheral nerve sheath tumors (MPNSTs) develop in patients with underlying NF1, and usually arise as a result of malignant transformation of a pre-existing plexiform neurofibroma. The clonal cytogenetic abnormalities reported in primary MPNST include complex karyotypes with chromosome numbers in the triploid or tetraploid range with recurrent abnormalities of several chromosomes including losses or imbalances. As a prelude to cell biological, pharmacological, and functional studies to investigate pathways and gene(s) associated with multistep tumorigenesis, which includes progression, metastasis and resistance to therapy in MPNST, detailed molecular cytogenetic and genetic analyses of cell lines from primary, metastatic and recurrent MPNST with underlying NF1 disorder have been performed. The clonal cytogenetic abnormalities detected in the primary tumor cell line were similar to those observed in primary cultures of this tumor. Due to the complexity of the rearrangements seen by G-banded karyotype analysis, further characterization of the clonal abnormalities in these three cell lines was performed by molecular cytogenetic techniques, including CGH and SKY. CGH analysis detected recurrent deletions of 9p, 12q21-q32, complete losses of the X-chromosome, and gains of the chromosomal segment 17q25 in all three cell lines. SKY analysis detected extensive clonal abnormalities in these cell lines. The nature and the alterations of the cell cycle regulators, particularly those associated with G1-S checkpoints and known to be deregulated in MPNST, were studied. These cell cycle regulators included those associated with Rb1-cyclin D1 and the p53 pathways. The findings are consistent with the argument that an imbalance between the cyclin activators of CDKs and inhibitory proteins such as p16 result in uncontrollable proliferation in the cell lines, associated with progression of the disease. LOH and expression of the p53 gene in metastatic and recurrent cell lines was observed, as reported by others. The role of biallelic inactivation of p53 gene in MPNST with underlying NF1 mutations, however, needs further study. Overexpression of Rb1-protein observed in metastatic and recurrent cell lines is indicative of its role in the progression of the disease. One of the most important observations of this study is that Nm23-H1 expression is closely associated with advanced or metastatic disease. In summary, MPNST cell lines derived from a patient with metastatic and recurrent disease with NF1 disorder were characterized and a gene associated with metastatic potential which is amenable to therapeutic and chemo-preventative approaches was identified. These cell lines with extensive characterization of genetic abnormalities are likely to provide important reagents for biochemical, molecular and pharmacological studies related to MPNST.