Skip to main content
. 2009 Dec 7;38(5):e29. doi: 10.1093/nar/gkp1138

Table 1.

Characteristics of PCR performance of various FRET technologies in the detection of SNP variations in the β2-macroglobulin gene

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.