Figure 1

Main window of FISH Oracle 2. Main window of FISH Oracle 2 focusing on the 10q23 locus which includes the tumor suppressor gene PTEN. Part (1) shows the search menu, which, in the displayed case, is used for searching a gene by its name. Part (2) consists of the toolbar showing different navigation and configuration options. Part (3) consists of the visualization area with the chromosome band below the genomic scale and four further tracks, one for Ensembl genes (in this case genes corresponding to Ensembl version 75 are displayed, indicated by the caption of the tab), one for CNVs (deletions in our case), one for SNVs and one for translocations, all displayed in default colors. All CNVs with a segment intensity value of less than -0.5 are shown. The SNV track displays several genes containing between one and seven SNVs followed by seven translocations in the next track. Each track shows a different data set (here obtained by microarrays and NGS), but all data refer to prostate cancer tissue samples. The most frequently occurring copy number changes form a minimal common region including the gene PTEN. Furthermore, PTEN is associated with seven SNVs in one dataset and three translocations in eleven samples of EO-PCA. The characteristic minimal common region derived from three different kinds of genomic events highlight the gene PTEN.