Figure 2

Genomic imbalances and gene rearrangement in soft tissue MMP tumors. (a) The pattern of genomic imbalances in four soft tissue MMP tumors and one pleomorphic adenoma (case 6) was heterogeneous and few recurrent aberrations were found. The individual cases are arranged in rows and the chromosomes in columns, separated by bars. Amplifications, gains and losses are shown in red, dark red and green, respectively. The genomic positions of the imbalances are presented in Table 4. (b) Case 2 showed amplifications of regions on chromosomes 6, 9 and 13 upon array CGH analysis. The individual bacterial artificial chromosome (BAC) clones are arranged according to their respective tumor/reference log 2 ratios on the y axis and their genomic location on the x axis. (c) The amplified material was found to be located in marker chromosomes, as shown by hybridization with whole chromosome paint (WCP) probes for chromosomes 6 (red), 9 (green) and 13 (blue). (d–f) Fluorescence in situ hybridization (FISH) analysis of gene rearrangements was performed using probes (indicated in red, green and blue) covering or partially covering the respective genes (indicated in yellow). In addition, WCP probes specific for selected chromosomes were used to discriminate normal cells from tumor cells. (d) EWSR1 on chromosome 22 was investigated using an EWSR1 break-apart probe (red and green). Case 5 displayed intact signals from this probe in 125 tumor nuclei, detected by three chromosomes 12 (green). (e) The HMGA2 gene on chromosome 12 was analyzed using the probes RP11-299L9 (green) and RP11-427K2 (red), respectively. In case 4, tumor cells identified by a WCP probe for chromosome 3 (green) showed a normal HMGA2 hybridization pattern. (f) Rearrangement of PLAG1 on chromosome 8 was studied using three, partially overlapping probes; RP11-246A9 (green), RP11-140I16 (red) and RP11-1130K23 (blue). In case 4, the PLAG1 gene was rearranged. The 5′ part of PLAG1 and regions upstream of the gene (blue) were translocated to a derivative chromosome 3. Chromosome 3 was detected by a red WCP probe (not shown) and therefore, the red signal on the derivative chromosome 8 possibly represented material from chromosome 3.