Table 2.
Comparison of array CGH genome profiles before and after Bst amplification
| Number of clones | Normal gene content | Gene amplification | Gene deletion | ||
| NSCLC 8 (2.9*) | |||||
| Before Bst MDA | 16277 | 12779 | 3450 | 48 | |
| Comparing after to before MDA | Matching clones | 13725 (84.3%) | 12592 (91.75%) | 1131 (8.24%) | 2 (<0.01%) |
| Clones that changed | 2552 (15.7%) | 187 (7.3%) | 2319 (90.9%) | 46 (1.8%) | |
| % of abnormal clones before MDA | 67.22% | 95.83% | |||
| NSCLC 9 (2.1*) | |||||
| Before Bst MDA | 23942 | 13538 | 9483 | 922 | |
| Comparing after to before MDA | Matching clones | 13960 (58.3%) | 13231 (94.8%) | 729 (5.2%) | 0 (0%) |
| Clones that changed | 9982 (41.7%) | 307 (3.1%) | 8754 (87.7%) | 922 (9.2%) | |
| % of abnormal clones before MDA | 92.31% | 100% | |||
Data from each of the four array CGH experiments (NSCLC 8 & 9 before and after Bst amplification) was normalized and replicate data points with standard deviation of log2 ratio > 0.075 were excluded. Following, data was analyzed with aCGH-Smooth software, which identifies breakpoints and areas of gene amplification and deletion. The numbers presented refer to clones that were evaluable both before and after Bst amplification for each of the tumors. * Highest ratio of un-amplified sample/reference.