High-resolution mapping of the N-myc amplicon core domain in neuroblastomas

The N-myc proto-oncogene is amplified in 25% of neuroblastomas. Amplification is strongly correlated with advanced disease stage and rapid tumor progression. We have constructed a detailed restriction map of the amplified core region in neuroblastomas which will allow the identification of structural features such as joint fragments, rearrangements and CpG islands. Using probes that had been obtained previously, twenty YACs were isolated from a library constructed from a double-minute-containing neuroblastoma cell line with 150-fold amplification of N-myc. Twenty-one YACs also were isolated from two normal human libraries. Normal and neuroblastoma YAC contiguous arrays (contigs), each spanning over 1 Mb of DNA, have been assembled (Molec Cell Biol 12:5563, 1992). A high-resolution restriction map of over 200 kb of contiguous DNA containing N-myc has been generated by subcloning YACs into cosmids. Using cosmids from this region plus additional amplified probes, we have determined that the amplicons from 33 neuroblastomas range in size from 350 kb to over 1 Mb. Rearrangements and deletions were identified in both tumors and cell lines. However joint fragments were not always amplified to the same level as the major amplicon, and may therefore represent a subset of amplicons. We have defined a 130 kb region which was amplified in 32 of the 33 tumors, and one additional tumor had deleted 65 kb of this region from its amplicon. The only CpG island found in this region was within the N-myc gene. Cosmids were screened with radiolabeled total cDNA probes and no highly expressed genes other than N-myc were found in the amplicon.