Table 5.
Comparison of QPCR and CARAT on HER2/neu locus across three cell lines.
| HER2/NEU Region on Chr 17 | |||||
| Sample | SNP 1720794 12.48 kb proximal | HER2/neu 38231.31–38259.79 kb | SNP 1738376 91.64 kb distal | ||
| CARAT | p-val | 2ΔCt + 1 | CARAT | p-val | |
| SK-BR-3 | 19.0 | <10-20 | 12.4 | 19.0 | <10-20 |
| ZR-75-30 | 25.1 | <10-20 | 27.7 | 25.1 | <10-20 |
| MCF-7 | 1.0 | 0.0003 | 0.8 | 2.1 | 0.567 |
Note:
12ΔCt + 1: theoretical estimate of total copy number using QPCR
2CARAT: copy number estimated by CARAT
3p-val: The statistical significance of the copy number alteration. It is derived from the algorithm by comparing the target sample to a reference set consisting of normal individuals