Figure 4.

Validation of optimized thresholds on additional array CGH data derived from the hypertriploid cervical SCC cell lines CaSki and SW756. Standard thresholds miss true single copy gains and losses detected by optimized thresholds and confirmed by FISH. Optimum thresholds (blue lines) call single copy changes of additional clones (red dots) classified as normal by the standard thresholds (green lines). Arrows in black or blue indicate the locations of clones selected for FISH validation that were correctly or wrongly classified by the optimum thresholds respectively. A: Log₂ ratio profile of chromosome 2 in CaSki. The optimum loss threshold (blue line) but not the standard loss threshold (green line) detects a single copy loss of clone RP11-114I18 located on 2q. FISH on a metaphase spread of CaSki confirms 1-copy loss (three copies) of clone RP11-114I18 (red) and four copies of the control clone RP11-526G13 (green). Arrows indicate the locations of clones (black dots) for which FISH confirmed that classification of loss using the optimum threshold was correct. B: Log₂ ratio profile of chromosome 7 in CaSki. The optimum gain threshold (blue line) but not the standard gain threshold (green line) detects a single copy gain of clone RP11-82A15. FISH on a metaphase spread of CaSki confirms 1-copy gain (five copies) of clone RP11-82A15 (green) and four copies of the control clone RP11-31N8 (red). Arrows indicate the locations of clones (cyan dots) selected for FISH validation. C: Log₂ ratio profile of chromosome 11 in SW756. The optimum loss threshold (blue line) but not the standard loss threshold (green line) detects a single copy loss of clone RP11-307I15. FISH on a metaphase spread of SW756 confirms 1-copy loss (three copies) of clone RP11-307I15 (red) and four copies of control clone RP11-509D23 (green). Arrows indicate the locations of clones (black dots) selected for FISH validation. D: Log₂ ratio profile of chromosome 7 in SW756. The optimum gain threshold (blue line) but not the standard gain threshold (green line) detects a single copy gain of clone RP11-008H7. FISH on a metaphase spread of SW756 confirms 1-copy gain (five copies) of clone RP11-008H7 (red) and four copies of the control clone RP11-81B20 (green). Arrows indicate the locations of clones (cyan dots) selected for FISH validation.