Table 1.
Assay type | Fluorescence background | Signal of match target at cycle 50 (background subtracted) | SNP discrimination factorsa |
|
---|---|---|---|---|
C/C mismatch | C/A mismatch | |||
Optimized Snake: | ||||
First position probe | 93 ± 4 | 1600 ± 39 | 0.46 ± 0.02 | 0.59 ± 0.02 |
Second position probe | 130 ± 5 | 1358 ± 45 | 1.00 ± 0.00 | 0.97 ± 0.00 |
Third position probe | 143 ± 5 | 1335 ± 38 | 0.95 ± 0.01 | 0.93 ± 0.02 |
Standard Snake: | ||||
First position probe | 100 ± 3 | 1220 ± 60 | 0.96 ± 0.01 | 0.92 ± 0.02 |
Second position probe | 130 ± 5 | 1210 ± 115 | 1.00 ± 0.00 | 0.99 ± 0.01 |
Third position probe | 150 ± 6 | 1370 ± 50 | 0.99 ± 0.00 | 0.99 ± 0.01 |
3′-MGB-Taqman: | ||||
14-mer | 120 ± 7 | 1010 ± 180 | 1.00 ± 0.00 | 0.94 ± 0.00 |
18-mer | 270 ± 9 | 790 ± 90 | 0.87 ± 0.01 | 0.81 ± 0.01 |
Taqman 22-mer | 200 ± 13 | 550 ± 60 | 0.78 ± 0.01 | 0.63 ± 0.04 |
Molecular Beacon | 110 ± 6 | 370 ± 30 | 0.31 ± 0.05 | 0.20 ± 0.10 |
Scorpion Primers: | ||||
21-mer | 250 ± 10 | 260 ± 30 | 0.24 ± 0.02 | 0.20 ± 0.14 |
15-mer | 190 ± 10 | 150 ± 10 | 0.93 ± 0.01 | 0.83 ± 0.04 |
aThe SNP discrimination factors for the individual technologies were calculated as 1-(Signal of mismatch/Signal of match), wherein the signal was measured at cycle 50 for all assays but optimized Snake. In optimized Snake, the SNP discrimination was measured at cycle 32.