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Table 8 Compared performance of QSS and other available methods

From: Quantitative Single-letter Sequencing: a method for simultaneously monitoring numerous known allelic variants in single DNA samples

Methods and associated references MSDa (%) MDb (%) R2
QSS 0.281 to 0.950 1.255 0.984 to 0.999
BAMPER [38] 3.8* ND 0.9999
Micro-Array [39, 40] 3.5 to 4.1 2.4 0.971 to 0.9921
Micro-Satellite [41] ND ND 0.97
Mass Spectrometry [29] 1.55 ND ND
PE+DHPLC [42] 1.4 1.2 0.977
Pyrosequencing [29, 43, 44] 0.07* to 1.9 ND 0.979 to 0.996
Quantitative Sequencing [28] 4.2 1.44 ND
RFLP [29] 2.8 ND ND
RFMP [25] ND ND 0.992
Single base extension [26, 29] 0.27 to 1.75 1.5 to 2.15 ND
SYBR Green [28, 45] 1.65 to 6.47 1 to 1.12 0.997
TaqMan Probe [28, 29, 46] 0.75 to 3.18 1.47 0.9984
  1. a Reproducibility is evaluated by the median of standard deviations (MSD) among repeats on different variants, and is expressed as a frequency in %. For QSS, the overall MSD is 0.401%; the values shown here, 0.281 and 0.950% are calculated from Table 4 (plasmid mix) and Table 5 (viral DNA population extracted from plant), respectively.
  2. b Accuracy is estimated i) by the median deviation (MD), being the median of all differences between observed and expected allele frequencies, and ii) by the correlation coefficient between observed and expected frequencies (R2).
  3. ND: Not-Determined
  4. (*) these values refer to standard deviation (SD), because the data available in the literature do not allow calculation of the MSD.