Table 2.
Specificity of DNase-chip, as assessed against gold-standard negative DNase I hypersensitive sites derived by real-time PCR of random segments (n = 134 for CD4+ T cells, n = 146 for GM06990 cells)
| Cell line | DNase I concentrations | Total number of sites detected by DNase-chip | Number of sites detected by DNase-chip that fall within a gold-standard negative site | Specificity |
|---|---|---|---|---|
| CD4+ T cells | ABC | 378 | 0/134 | ~100% |
| AB | 134 | 1/134 | 99% | |
| AC | 174 | 0/134 | ~100% | |
| BC | 200 | 0/134 | ~100% | |
| A only | 981 | 2/134 | 99% | |
| B only | 836 | 0/134 | ~100% | |
| C only | 547 | 3/134 | 98% | |
| Averaged | 1,264 | 4/134 | 97% | |
| GM06990 cells | ABC | 172 | 0/146 | ~100% |
| AB | 64 | 1/146 | 99% | |
| AC | 112 | 1/146 | 99% | |
| BC | 159 | 0/146 | ~100% | |
| A only | 712 | 9/146 | 94% | |
| B only | 777 | 4/146 | 97% | |
| C only | 504 | 2/146 | 99% | |
| Averaged | 1,100 | 5/146 | 97% |