Figure 4

Chr3 rearrangements in UOK147 cell line based on comparison of array-CGH and mpFISH results. A. Chr3 painting probe identifies different chr3 fragments (green) on the rearranged marker chromosomes (M1, M2,...M8).B and C. Interphase (B) and metaphase (C) mpFISH illustration of a pericentromeric rearrangement. Clones RP11-356G4 (red) at 3p11, and RP11-13K6 (green) at 3q11, frame the centromere of chr3. Note the split signal indicating insertion in M1 and loss of red signal indicating loss of 3p through an imbalanced translocation in M2. D. Schematic results of chr3 rearrangements detected by mpFISH. Bars represent chr3 fragments found within the marker chromosomes (M1, M2,...M8). tr: unbalanced translocation breakpoint; b tr: balanced translocation; dup: duplication; id: interstitial deletion; ins: insertion of other chromosome fragment. E. Array-CGH profile. X-axis: displays 179 chr3 BAC clones ordered from 3pter (left) to 3qter (right). Y-axis: normalized fluorescence ratio (NFR). Each spot represents an average between at least two replicas of each clone on the array (see Methods). According to mpFISH we defined specific chr3 regions (R1, R2,...R10) of certain copy number: R1 ANILFR ± 1 sd; 1.07 ± 0.06 corresponds to 4 copies; R2 ANILFR ± 1 sd; 0.61 ± 0.03 corresponds to 2 copies a.s.o (see Table 1). Orange line represents the ANILFR (Average Normalized Inter-Locus Fluorescence Ratio) value and yellow lines frames the double standard deviation intervals for each region (Methods). (see Table 1). (Note: the measurement points from individual PAC/BAC clones, which reside outside the double standard deviation, must be confirmed by FISH to be able to rely on them. In this case FISH confirmed only one single clone change -R4).