Table 2.
Sample Raw DNA Concentrations and Proportion of Amplifiable DNA
| DNA samples | Raw DNA concentration (ng/μl) | Amplifiable fraction of raw DNA input | ||||
|---|---|---|---|---|---|---|
| ABR | D17S695 | D17S678 | ||||
| DNA derived from frozen tumors and matching buffy coat samples | Frozen-1-normal | 170.4 | 1:1 | 1:3 | 1:2 | |
| Frozen-1-tumor | 327.8 | 1:1 | 1:5 | 1:2 | ||
| Frozen-2-normal | 21 | 1:1 | 1:3 | 1:2 | ||
| Frozen-2-tumor | 41.2 | 1:1 | 1:3 | 1:1 | ||
| Frozen-3-normal | 1.8 | 1:1 | 1:1 | 1:2 | ||
| Frozen-3-tumor | 5.4 | 1:1 | 1:3 | 1:2 | ||
| Frozen-4-normal | 54.8 | 1:1 | 1:1 | 1:2 | ||
| Frozen-4-tumor | 305.8 | 1:1 | 1:3 | 1:2 | ||
| Frozen-5-normal | 79 | 1:2 | 1:1 | 1:2 | ||
| Frozen-5-tumor | 115.6 | 1:1 | 1:3 | 1:1 | ||
| FFPE-derived samples without PCR-amplification problems in previous LOH studies | FFPE-1-normal | 29 | 1:2,417 | 1:3,625 | FTA* | |
| FFPE-1-tumor | 12.6 | 1:20 | 1:325 | FTA* | ||
| FFPE-2-normal | 2.6 | 1:6 | 1:25 | 1:78 | ||
| FFPE-2-tumor | 28.2 | 1:46 | 1:243 | FTA* | ||
| FFPE-3-normal | 5.6 | 1:40 | 1:58 | 1:199 | ||
| FFPE-3-tumor | 13.4 | 1:16 | 1:77 | 1:353 | ||
| FFPE-4-normal | 7.2 | 1:1,800 | 1:153 | FTA* | ||
| FFPE-4-tumor | 9.4 | 1:58 | 1:41 | 1:855 | ||
| FFPE-5-normal | 7.4 | 1:12 | 1:31 | 1:58 | ||
| FFPE-5-tumor | 10.8 | 1:14 | 1:46 | 1:77 | ||
| FFPE-derived samples with PCR-amplification problems in previous LOH studies | FFPE-6-normal | 0.8 | FTA* | FTA* | FTA* | |
| FFPE-6-tumor | 2.6 | FTA* | FTA* | FTA* | ||
| FFPE-7-normal | 2 | FTA* | FTA* | FTA* | ||
| FFPE-7-tumor | 2.8 | 1:7 | 1:110 | FTA* | ||
| FFPE-8-normal | 2.4 | 1:27 | FTA* | FTA* | ||
| FFPE-8-tumor | 7.6 | FTA* | FTA* | FTA* | ||
| FFPE-9-normal | 5.2 | 1:28 | 1:166 | FTA* | ||
| FFPE-9-tumor | 1 | 1:5 | 1:56 | FTA* | ||
| FFPE-10-normal | 4.2 | 1:6 | 1:500 | FTA* | ||
| FFPE-10-tumor | 6.6 | 1:1,031 | FTA* | FTA* | ||
, FTA = failed to amplify.