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Table 1 Ratio of the observed number of molecules with mismatch primers relative to the average number of molecules with perfect match primer pairs.

From: Evaluation of the impact of single nucleotide polymorphisms and primer mismatches on quantitative PCR

  QIAGEN ROCHE
Primer Pairs1 (5' – 3') Observed Effect2 Predicted Effect3 Observed Effect2 Predicted Effect3
Clone GQ0068_E07 (G-G)
T1 – PM 0.021   0.40  
T2 – PM 0.20   0.79  
T3 – PM 1.2   0.94  
PM – A1 1.0   1.2  
PM – A2 0.019   0.52  
T1-A1 0.022 0.021 0.49 0.47
T1-A2 0.00047 0.00039 0.14 0.21
T2-A1 0.24 0.21 1.1 0.93
T2-A2 0.0045 0.0037 0.35 0.41
T3-A1 1.3 1.2 1.4 1.1
T3-A2 0.025 0.022 0.44 0.49
Clone GQ0065_F11 (T-G)
G1 – PM 0.089   0.79  
G2 – PM 0.68   1.3  
G3 – PM 1.1   1.1  
PM – A1 1.1   1.1  
PM – A2 0.024   0.45  
G1-A1 0.10 0.098 1.1 0.90
G1-A2 0.0024 0.0021 0.56 0.35
G2-A1 0.66 0.74 1.4 1.4
G2-A2 0.013 0.016 0.58 0.56
G3-A1 1.0 1.2 1.5 1.2
G3-A2 0.022 0.027 0.64 0.48
Clone GQ00612_A24 (G-T)
T1 – PM 0.023   n.d.4  
T2 – PM 0.20   n.d.  
T3 – PM 1.2   n.d.  
PM – C1 0.87   n.d.  
PM – C2 0.0062   n.d.  
T1-C1 0.018 0.020 n.d.  
T1-C2 0.00012 0.00014 n.d.  
T2-C1 0.15 0.17 n.d.  
T2-C2 0.0015 0.0012 n.d.  
T3-C1 0.95 1.1 n.d.  
T3-C2 0.0075 0.0076 n.d.  
  1. 1 Primer pairs with one mismatch primer containing in a single oligonucleotide substitution in combination with one perfect match primer (PM) are used to evaluate the effect of SNP (observed effect) on qPCR quantifications.
  2. 2 Observed effects are expressed as a ratio of quantified molecules relative to the number of molecules quantified with perfect match primer pairs.
  3. 3 Predicted effects are calculated when two mismatch primers are used, by multiplying the observed effect of each of the two single mismatch primers. For example the predicted effect of the T1-A1 (0.021) primer pair on clone GQ0068_E07 is equal to the product of the observed effects of T1 (T1-PM, 0.021) and A1 (PM-A1, 1.0). There is strong agreement between the observed and predicted effects.
  4. 4 not determined