Table 1.
PCR-Based SNP Genotyping Assay Comparison
| Estimated Reagent Cost and Throughput (per 96-well plate) | |||||
|---|---|---|---|---|---|
| ARMS-PCR | Small Amplicon | Blocked Probe | RFLP | ||
| Reagents ($) | |||||
| Taq / dNTP | 100 | 100 | 100 | 100 | |
| Primers / Probe | 2 | 1 | 2 | 1 | |
| Analysis | 2 | 10 | 10 | 22 | |
| Total Cost | 104 | 111 | 112 | 123 | |
| Time (Minutes) | |||||
| PCR Setup | 30 | 30 | 30 | 30 | |
| Cycling | 90 | 75 | 75 | 90 | |
| Handling | 30 | 0 | 0 | 45 | |
| Endonuclease | 0 | 0 | 0 | 60 | |
| Electrophoresis | 60 | 0 | 0 | 60 | |
| Analysis | 15 | 15 | 15 | 15 | |
| Total Time | 225 | 120 | 120 | 300 | |
| Bbaa2 Genotyping (26 positions, 96-well plates, run back-to-back) | |||||
| ARMS-PCR | Small Amplicon | Blocked Probe | RFLP | ||
| 9 Unknowns + 3 Control Samples | |||||
| Total Cost ($) | 340 | 360 | 365 | 400 | |
| Total Time (Hrs) | 15 | 8 | 8 | 20 | |
| 21 Unknowns + 3 Control Samples | |||||
| Total Cost ($) | 675 | 720 | 730 | 800 | |
| Total Time (Hrs) | 27 | 14 | 14 | 35 | |
| Assay Design / Utility | |||||
| ARMS-PCR | Small Amplicon | Blocked Probe | RFLP | ||
| Success Rate | 10% (1/10) | 81% (9/11) | 75% (12/16) | Not Tested | |
| Interpretation | Unequivocal | Subjective* | Unequivocal | Unequivocal | |
*
An objective genotype assignment can be made by spiking unclear samples with control DNA and repeating the HRMA