Table 2. Comparison of the accuracy of the three methods in estimating allele frequencies in a pool of 96 DNAs (Pool96).
| Marker | Sample frequency | Estimated frequency | ||
|---|---|---|---|---|
| SnaPshot™ | dHPLC | MassARRAY™ | ||
| RS15020285 | 0.658 | 0.666 ± 0.022 (0.007) | 0.633 ± 0.013 (0.004) | 0.727 ± 0.013 (0.004) |
| RS508509 | 0.714 | 0.702 ± 0.135 (0.043) | 0.711 ± 0.013 (0.004) | 0.761 ± 0.009 (0.003) |
| RS1402045 | 0.713 | 0.699 ± 0.047 (0.015) | 0.683 ± 0.047 (0.015) | 0.724 ± 0.009 (0.003) |
| RS643304 | 0.657 | 0.648 ± 0.032 (0.010) | 0.656 ± 0.022 (0.007) | 0.645 ± 0.013 (0.004) |
| RS489009 | 0.528 | 0.561 ± 0.063 (0.02) | 0.501 ± 0.054 (0.017) | 0.503 ± 0.009 (0.003) |
The sample allelic frequencies were obtained from genotyping the 96 individuals (using the SNaPshot™ method). A k correction factor for unequal amplification was obtained for each of the three methods and used to estimate the frequencies in the Pool96. Ten replicates of Pool96 were genotyped to test the repeatability of the method, which is expressed here as ± standard deviation (and SEM).