Supplementary Material for: Integrated Cytogenetic and High-Resolution Array CGH Analysis of Genomic Alterations Associated with <i>MYCN</i> Amplification A.Pandita J.Bayani J.Paderova P.Marrano C.Graham M.Barrett M.Prasad M.Zielenska J.A.Squire 2011 Amplification of oncogenes and closely linked flanking genes is common in some types of cancer and can be associated with complex chromosome rearrangements and/or co-amplification of non-syntenic chromosomal regions. To better understand the etiology and structural complexity of focal <i>MYCN</i> amplicons in human neuronal cancer, we investigated the precise chromosomal locations of high copy number genomic regions in <i>MYCN</i> amplified cell lines. An integrated cytogenetic map of the <i>MYCN</i> amplicon was created using high-resolution array CGH, spectral karyotyping (SKY), multi-color banding (mBAND), and fluorescence in situ hybridization (FISH) in 4 human neuronal tumor cell lines. The evidence of complex intra- and inter-chromosomal events, providing clues concerning the nature of the genomic mechanisms that contributed to the process of <i>MYCN</i> amplification, was observed. The presence of multiple co-amplified syntenic or non-syntenic sequences in the <i>MYCN</i> amplicon is quite intriguing. <i>MYCN</i> is usually centrally located in the amplicon; however, the structure and complexity of the amplicons were highly variable. It is noteworthy that clusters of unstable repetitive regions characterized by CNV sequences were present throughout the regions encompassed by <i>MYCN</i> gene amplification, and these sequences could provide a mechanism to destabilize this region of the genome. Complex structural rearrangements involving genomic losses and gains in the 2p24 region lead to <i>MYCN</i> amplification and that these rearrangements can trigger amplification events.