Table 2. Sensitivity, specificity and AUROC of genotypic algorithms for predicting coreceptor usage of test set V3 sequences.
| PhenoSeq | g2p FPR 5.75% | g2p FPR 10% | WebPSSMX4R5 | WebPSSMSI/NSI* | ||
|---|---|---|---|---|---|---|
| PhenoSeq-B Test Set 1 | Sens/Spec | 100/87.8 | 100/97.6 | 100/90.2 | 41.7/95.1 | 16.7/87.8 |
| Mulinge et al | AUROC | 0.94 | 0.99 (p = 0.17) | 0.95 (p = 0.44) | 0.68 (p < 0.01) | 0.52 (p < 0.01) |
| 12 CXCR4-using, 41 R5 | ||||||
| PhenoSeq-B Test Set 2 | Sens/Spec | 78.4/80.3 | 70.7/92.2 | 72.8/84 | 55.4/96.3 | 62/94.1 |
| Los Alamos HIV Database | AUROC | 0.79 | 0.82 (p = 0.32) | 0.78 (p = 0.41) | 0.76 (p = 0.24) | 0.78 (p = 0.41) |
| 92 CXCR4-using, 269 R5 | ||||||
| PhenoSeq-C Test Set 1 | Sens/Spec | 83.6/92.5 | 78.2/95 | 81.8/95 | - | 85.5/77.5 |
| A4001064 | AUROC | 0.88 | 0.87 (p = 0.22) | 0.88 (p = 0.30) | - | 0.82 (p = 0.22) |
| 55 CXCR4-using, 40 R5 | ||||||
| PhenoSeq-C Test Set 2 | Sens/Spec | 77.8/75.4 | 11.1/93 | 50/82.4 | - | 61.1/81.3 |
| MERIT | AUROC | 0.77 | 0.52 (p < 0.01) | 0.66 (p = 0.15) | - | 0.71 (p = 0.29) |
| 18 CXCR4-using, 187 R5 | ||||||
| PhenoSeq-D Test Set | Sens/Spec | 80.5/77.3 | 81.4/72.7 | 88.4/61.4 | 81.4/65.9 | 69.8/63.6 |
| A4001064 | AUROC | 0.79 | 0.77 (p = 0.40) | 0.75 (p = 0.29) | 0.74 (p = 0.24) | 0.67 (p = 0.05) |
| 43 CXCR4-using, 44 R5 | ||||||
| PhenoSeq-AE Test Set | Sens/Spec | 85.7/96 | 78.6/68 | 85.7/56 | 85.7/72 | 85.7/76 |
| A4001064 | AUROC | 0.91 | 0.73 (p = 0.046) | 0.71 (p = 0.03) | 0.79 (p = 0.11) | 0.81 (p = 0.15) |
| 14 CXCR4-using, 25 R5 | ||||||
| PhenoSeq-A/AG Test Set 1 | Sens/Spec | 88.9/76.8 | 44.4/97.1 | 55.6/94.2 | 44.4/87 | 66.7/84 |
| A4001064 | AUROC | 0.83 | 0.71 (p = 0.18) | 0.75 (p = 0.27) | 0.66 (p = 0.10) | 0.75 (p = 0.28) |
| 9 CXCR4-using, 69 R5 | ||||||
| PhenoSeq-A/AG Test Set 2 | Sens/Spec | 62.5/97.2 | 50/94.4 | 62.5/80.6 | 37.5/88.9 | 37.5/91.7 |
| Mulinge et al | AUROC | 0.80 | 0.72 (p = 0.30) | 0.72 (p = 0.29) | 0.63 (p = 0.14) | 0.65 (p = 0.16) |
| 8 CXCR4-using, 36 R5 |
Sens (% sensitivity) and Spec (% specificity) was calculated as described in the Table 1 legend. P-values (two-tailed) for comparisons of area under the receiver operator characteristic curve (AUROC) were performed according to Hanley et al33. P-values < 0.05 were considered significant and are highlighted in bold italicized text. FPR, false positive rate.
*The subtype C specific WebPSSMSI/NSI algorithm was used for subtype C HIV-1 predictions.