Table 3.
Evaluation of Several Genotypic Tools for the Prediction of CXCR4 Usage
| |
Prediction of CXCR4 usagea |
|||
|---|---|---|---|---|
| Genotypic tool | Sensitivity (%) | Specificity (%) | PPV (%) | NPV (%) |
| 11/25 charge rule | 30.0 | 96.9 | 83.0 | 74.0 |
| Net V3 charge rule | 65.0 | 78.1 | 59.0 | 82.0 |
| C-PSSMsinsi | 75.0 | 87.5 | 75.0 | 88.0 |
| Geno2pheno[coreceptor]b | 60.0 | 87.5 | 70.0 | 82.0 |
| Combined rulesc | 63.2 | 100.0 | 100.0 | 85.0 |
| C4.5 | 25.0 | 100.0 | 100.0 | 73.0 |
| C4.5 positions 8–12 | 25.0 | 100.0 | 100.0 | 73.0 |
| PART | 30.0 | 100.0 | 100.0 | 75.0 |
| SVMwetcat | 40.0 | 96.9 | 86.0 | 77.0 |
a
A total of 52 pure subtype C isolates with both phenotypic and genotypic data were included in this analysis.
b
A false-positive rate of 10% was used.
c
A combination of the first four genotypic tools was used where the majority prediction was considered as the final genotype prediction (n=47). PPV, positive predictive value; NPV, negative predictive value.