Table 2. Optimisation of DNA Labelling Protocol.
| Sample | Tissue Type | Amount of DNA Used (µg) | ULS-Dye Used | DNA to dye ratio (µg/µl) | Post Labelling DNA Yield (µg) | Degree of Labelling (%) | Labelling Pass/Fail | Dye Signal Intensity on Array |
| A - Labelling reactions carried out using hot blocks and water baths | ||||||||
| 1 | FFPE | 0.5 | Cy5 | 1.0 | 0.49 | 0.4 | Fail | *NP |
| 2 | FFPE | 0.5 | Cy5 | 1.0 | 0.5 | 0.2 | Fail | *NP |
| 3 | FFPE | 0.5 | Cy5 | 1.0 | 0.5 | 0.23 | Fail | *NP |
| 4 | FFPE | 0.5 | Cy5 | 1.0 | 0.66 | 0.36 | Fail | *NP |
| 5 | Control DNA | 0.5 | Cy3 | 1.0 | 0.45 | 0.45 | Fail | *NP |
| 6 | Control DNA | 0.5 | Cy3 | 1.0 | 0.45 | 0.45 | Fail | *NP |
| 7 | Control DNA | 0.5 | Cy3 | 1.0 | 0.39 | 0.39 | Fail | *NP |
| 8 | Control DNA | 0.5 | Cy3 | 1.0 | 0.56 | 0.56 | Fail | *NP |
| B - Labelling reactions carried out using thermal cycler | ||||||||
| 9 | FF | 0.5 | Cy5 | 1.0 | 0.89 | 2.01 | Pass | 99 |
| 10 | FFPE | 0.5 | Cy5 | 1.0 | 0.72 | 2.39 | Pass | 94 |
| 11 | FFPE | 0.5 | Cy5 | 1.0 | 0.59 | 3.27 | Pass | 79 |
| 12 | Control DNA | 0.5 | Cy3 | 1.0 | 0.73 | 1.08 | Fail | *NP |
| 13 | Control DNA | 0.5 | Cy3 | 1.0 | 0.68 | 1.15 | Fail | *NP |
| 14 | Control DNA | 0.5 | Cy3 | 1.0 | 0.88 | 0.97 | Fail | *NP |
| 15 | Control DNA | 0.5 | Cy3 | 1.0 | 0.83 | 2.15 | Pass | 153 |
| 16 | Control DNA | 0.5 | Cy3 | 1.0 | 0.78 | 2.19 | Pass | 148 |
| 17 | Control DNA | 0.5 | Cy3 | 1.0 | 0.82 | 2.19 | Pass | 103 |
| C - Labelling reactions carried out using thermal cycler and excess dye | ||||||||
| 18 | FFPE | 0.8 | Cy5 | 0.8 | 0.8 | 2.24 | Pass | 307 |
| 19 | FFPE | 0.8 | Cy5 | 0.8 | 0.6 | 2.32 | Pass | 245 |
| 20 | FFPE | 0.8 | Cy5 | 0.8 | 0.64 | 1.56 | Pass | 275 |
| 21 | FFPE | 0.8 | Cy3 | 0.8 | 0.91 | 2.04 | Pass | 383 |
| 22 | Control DNA | 0.8 | Cy3 | 0.8 | 0.95 | 3.08 | Pass | 1503 |
| 23 | Control DNA | 0.8 | Cy3 | 0.8 | 0.81 | 3.07 | Pass | 1251 |
| 24 | Control DNA | 0.8 | Cy3 | 0.8 | 0.76 | 3.1 | Pass | 1228 |
| 25 | Control DNA | 0.8 | Cy3 | 0.8 | 0.87 | 3.11 | Pass | 1403 |
*
NP – Array CGH not performed on sample (if sample failed on spectrophotometry). Spectrophotometry for DNA concentration and Degree of Labelling (DoL) done using Nanodrop® ND-2000 and optimal DoL = 0.75–2.5% (for ULS- Cy5); or 1.75–3.5% (for ULS Cy3). Dye Signal Intensity calculated as part of Quality Control Metrics by Agilent Feature Extraction Software (v10.7.3).