Table 7.
Comparison of three existing tools used to identify exonic SAVs with MutPred Splice
| Method | ANNOVAR | Human splicing finder | Skippy | MutPred splice |
|---|---|---|---|---|
| Splicing focus |
Splice site disruption |
All exonic and intronic |
ESE/ESS disruption and cryptic splice site |
All exonic |
| Prediction output |
Binary label |
Multiple output scores |
Multiple output scores |
Probabilistic, with additional hypothesis of splicing mechanism disrupted |
| TP |
41 |
65 |
68 (61) |
121 |
| FP |
4 |
33 |
15 |
7 |
| TN |
79 |
50 |
68 |
76 |
| FN |
140 (0) |
116 |
113 (57) |
60 |
| FPR% |
4.8 |
39.8 |
18.1 |
8.4 |
| Sensitivity (%) |
22.7 (100.0) |
35.9 |
37.6 (51.7) |
66.9 |
| Specificity (%) |
95.2 |
60.2 |
81.9 |
91.6 |
| Accuracy (%) |
58.9 (97.6) |
48.1 |
59.7 (66.8) |
79.2 |
| MCC | 0.22 (0.93) | -0.04 | 0.19 (0.34) | 0.54 |
Evaluation was based on 264 exonic variants (181 positive, 83 negative). Performance metrics are given for guidance only as not all tools may be directly comparable (due to different applications or limitations). Performance scores in parentheses reflect adjusted performance based upon the evaluation of only specific categories of splicing mutation (for example, splice site disruption) relevant to the respective tool. For methods that output multiple scores for a variant (HSF and Skippy), performance metrics may differ depending upon the features and thresholds applied. TP, true positives; FP, false positives; TN, true negatives; FN, false negatives; FPR, false positive rate; MCC, Matthews correlation coefficient.