Table 1.
Call Rates and Reproducibility of the Dynamic Array for Scale-up Genotyping of 1698 Samples against 24 SNPs
| SNP | CH samples (n = 461) |
KK samples (n = 1237) |
||
|---|---|---|---|---|
| Call rate (%) | Reproducibility (%) | Call rate (%) | Reproducibility (%) | |
| Avg | 99.2 | 99.4 | 97.6 | 96.3 |
| 1 | 100 | 99.8 | 99.7 | 96.2 |
| 2 | 99.7 | 99.1 | 99.2 | 94.3 |
| 3 | 98 | 98.5 | 89.5 | 95.3 |
| 4 | 99.8 | 100 | 96.4 | 97.3 |
| 5 | 99.1 | 98.7 | 99.4 | 98.5 |
| 6 | 100 | 100 | 99.3 | 95.5 |
| 7 | 100 | 100 | 99.3 | 97.6 |
| 8 | 99.9 | 98.9 | 95.8 | 95.6 |
| 9 | 99.7 | 99.3 | 97.9 | 94.7 |
| 10 | 100 | 100 | 99.6 | 98.1 |
| 11 | 99 | 99.8 | 98.6 | 94 |
| 12 | 99.6 | 99.1 | 97.9 | 91.5 |
| 13 | 98.2 | 99.3 | 99.2 | 96 |
| 14 | 99.7 | 99.6 | 99.4 | 97.5 |
| 15 | 99.9 | 99.8 | 95.3 | 97.6 |
| 16 | 99.7 | 99.6 | 99.5 | 95.7 |
| 17 | 94 | 98.9 | (76.7)⁎ | (93.8)⁎ |
| 18 | 99.7 | 99.3 | 99.7 | 98.4 |
| 19 | 98.9 | 99.6 | 94.7 | 97.7 |
| 20 | (31.8)⁎ | (97.6)⁎ | (6.2)⁎ | (94.1)⁎ |
| 21 | 99.9 | 99.8 | 99.2 | 96.8 |
| 22 | 98 | 99.3 | 93.5 | 97 |
| 23 | 99.8 | 97.6 | 97.3 | 96.7 |
| 24 | 98 | 99.6 | 96.8 | 97.1 |
The performance indicators used to evaluate the genotyping platforms were defined according to the following formulae: i) Call rate (%) = (No. of successful base calls)/(Total no. of assays performed) × 100 and ii) Reproducibility between replicates (%) = {1 − [(No. of assays inconsistent between replicates)/(Total no. of assays)]} × 100.
⁎
Values in parentheses were excluded from the overall rate computations as they had failure rates of >19%.