Table 5.
Relative Copy Number for Each Gene or Region Was Calculated as Follows: Deletion: ≤ Copy Number of Controls Minus 95% Reference Range of Controls (or 2SD of Controls), Gain: ≥ Copy Number of Controls Plus 95% Reference Range of Controls (or 2SD of Controls).
| Tumor | 1p36.32 (RP4-703E10) | BCL7B* | BCL7A (RP11-87C12) | 14q12 (RP11-125A5) | FOXG1B Promoter† |
|---|---|---|---|---|---|
| BAC array/RT-QPCR | BAC array/RT-QPCR | BAC array/RT-QPCR | BAC array/RT-QPCR | RT-QPCR | |
| IN1740 | Loss/0.54 | No CNA/0.38 | No CNA/0.53 | No CNA/0.71 | 0.50 |
| IN2356 | ND/0.85 | ND/0.88ND/0.79 | ND/0.62 | 1.07 | |
| IN2368 | No CNA/1.05 | Loss/0.31 No | CNA/0.85 | Loss/0.89 | 1.12 |
| IN2524 | Gain/1.22 | Loss/1.08 | No CNA/1.01 | Loss/0.33 | 1.30 |
| IN2631 | Gain/1.17 | No CNA/0.24 | No CNA/1.10 | Loss/1.10 | 0.95 |
| IN2674 | Loss/0.85 | Loss/0.48 | No CNA/0.51 | Loss/0.85 | 1.04 |
| IN2788 | Loss/0.37 | Loss/0.23 | No CNA/0.29 | No CNA/0.74 | 0.32 |
| IN2825 | ND/0.99 | ND/0.66 | ND/0.67 | ND/0.96 | 0.69 |
| IN2921 | ND/0.93 | ND1.03 | ND/0.34 | ND/0.90 | 0.38 |
| IN2940 | Loss/1.10 | No CNA/0.59 | No CNA/0.44 | Loss/1.01 | 0.49 |
| IN2969 | Gain/0.61 | No CNA/0.52 | No CNA/0.48 | Loss/0.91 | 0.55 |
| IN3013 | Loss/0.46 | Loss/0.44 | No CNA/0.35 | Loss/0.47 | 0.32 |
| IN3115 | Gain/1.12 | Loss/0.33 | Loss/0.38 | Loss/0.98 | 1.06 |
| IN3156 | ND/0.33 | ND/0.35 | ND/0.34 | ND/0.28 | 0.48 |
BAC clone alterations for each region are indicated by loss or gain. Blue values correspond to deletions detected by RT-QPCR. Red values correspond to gains detected by RT-QPCR.
*
BCL7B is not located under a specific clone but maps within the small region of loss encompassing up to seven clones at 7q11.23. ND indicates not done.
†
FOXG1B maps adjacent to clone RP11-125A5 at 14q12.