Table 4.
Number of Informative SNPs and LOH by Chromosome, Identified in the Fixed and Frozen Samples from Two Cases of Breast Cancer
| Chromosome | Case 1 | Case 2 | |||
|---|---|---|---|---|---|
| Frozen tissue LOH†/informative* (DI = 1.43) | Fixed tissue | Frozen tissue LOH/informative (DI = 1.79) | Fixed tissue LOH/informative (DI = 1.76) | ||
| LOH/informative (DI = 1.49) | LOH/informative (DI = 1.82) | ||||
| 1 | 1 /27 | 0 /26 | 2 /26 | 0 /32 | 0 /28 |
| 2 | 8 /26 | 10 /25 | 9 /25 | 1 /29 | 1 /23 |
| 3 | 12 /26 | 11 /28 | 13 /28 | 0 /36 | 0 /25 |
| 4 | 11 /16 | 3 /16 | 12 /16 | 0 /22 | 0 /15 |
| 5 | 1 /17 | 1 /17 | 1 /17 | 0 /14 | 0 /10 |
| 6 | 20 /33 | 19 /35 | 21 /35 | 0 /27 | 1 /26 |
| 7 | 1 /16 | 1 /16 | 2 /16 | 0 /21 | 0 /19 |
| 8 | 0 /33 | 0 /33 | 1 /33 | 18 /36 | 15 /27 |
| 9 | 5 /22 | 5 /22 | 4 /22 | 0 /17 | 0 /15 |
| 10 | 7 /10 | 8 /12 | 9 /12 | 0 /20 | 1 /15 |
| 11 | 17 /20 | 0 /21 | 6 /21 | 5 /23 | 4 /22 |
| 12 | 2 /18 | 1 /18 | 3 /18 | 0 /6 | 0 /6 |
| 13 | 0 /14 | 0 /11 | 1 /11 | 0 /8 | 0 /5 |
| 14 | 0 /9 | 0 /9 | 0 /9 | 1 /13 | 1 /10 |
| 15 | 0 /16 | 0 /17 | 1 /17 | 0 /16 | 0 /14 |
| 16 | 0 /11 | 0 /12 | 1 /12 | 6 /11 | 6 /8 |
| 17 | 19 /20 | 18 /21 | 21 /21 | 6 /15 | 6 /13 |
| 18 | 2 /13 | 3 /13 | 4 /13 | 7 /10 | 4 /7 |
| 19 | 0 /16 | 0 /17 | 1 /17 | 7 /17 | 1 /11 |
| 20 | 0 /5 | 0 /6 | 0 /6 | 0 /9 | 0 /6 |
| 21 | 0 /6 | 0 /6 | 0 /6 | 0 /8 | 0 /5 |
| 22 | 0 /6 | 0 /8 | 1 /8 | 5 /5 | 5 /5 |
| X | 0 /5 | 0 /6 | 5 /6 | 0 /7 | 0 /7 |
| Unmapped | 0 /2 | 1 /3 | 1 /3 | 0 /4 | 0 /2 |
| Total | 106/387 (27%) | 81/398 (20%) | 119/398 (30%) | 56/406 (14%) | 45/324 (14%) |
*SNP sites where the normal sample genotype call was AB (see Materials and Methods text).
†SNP sites which were informative in the normal and had either AA or BB genotype calls in the tumor sample (see Materials and Methods text).