Table 2 Evaluation of structural variant detection performance.
From: Targeted adaptive sampling enables clinical pharmacogenomics testing and genome-wide genotyping
SV type | DNA input (ng) | Basecalling model | Callability % (95% CI) | Concordance % (95% CI) | Sensitivity % (95% CI) | Specificity % (95 % CI) | Precision % (95 % CI) | TN | TP | FP | FN | NC | Total |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Deletion | 800 | HAC | 100.00 (82.41-100.00) | 94.44 (74.24-99.01) | 80.00 (37.55-96.38) | 100.00 (77.19-100.00) | 100.00 (51.01-100.00) | 13 | 4 | 0 | 1 | 0 | 18 |
SUP | 100.00 (82.41-100.00) | 100.00 (82.41-100.00) | 100.00 (56.55-100.00) | 100.00 (77.19-100.00) | 100.00 (56.55-100.00) | 13 | 5 | 0 | 0 | 0 | 18 | ||
1000 | HAC | 100.00 (90.36-100.00) | 100.00 (90.36-100.00) | 100.00 (56.55-100.00) | 100.00 (88.97-100.00) | 100.00 (56.55-100.00) | 31 | 5 | 0 | 0 | 0 | 36 | |
SUP | 100.00 (93.36-100.00) | 100.00 (93.36-100.00) | 100.00 (56.55-100.00) | 100.00 (92.73-100.00) | 100.00 (56.55-100.00) | 49 | 5 | 0 | 0 | 0 | 54 | ||
Duplication | 800 | HAC | 100.00 (82.41-100.00) | 100.00 (82.41-100.00) | 100.00 (43.85-100.00) | 100.00 (79.61-100.00) | 100.00 (43.85-100.00) | 15 | 3 | 0 | 0 | 0 | 18 |
SUP | 100.00 (82.41-100.00) | 100.00 (82.41-100.00) | 100.00 (43.85-100.00) | 100.00 (79.61-100.00) | 100.00 (43.85-100.00) | 15 | 3 | 0 | 0 | 0 | 18 | ||
1000 | HAC | 100.00 (90.36-100.00) | 100.00 (90.36-100.00) | 100.00 (51.01-100.00) | 100.00 (89.28-100.00) | 100.00 (51.01-100.00) | 32 | 4 | 0 | 0 | 0 | 36 | |
SUP | 100.00 (93.36-100.00) | 100.00 (93.36-100.00) | 100.00 (51.01-100.00) | 100.00 (92.87-100.00) | 100.00 (51.01-100.00) | 50 | 4 | 0 | 0 | 0 | 54 | ||
Hybrid | 800 | HAC | 100.00 (82.41-100.00) | 100.00 (82.41-100.00) | 100.00 (70.09-100.00) | 100.00 (70.09-100.00) | 100.00 (70.09-100.00) | 9 | 9 | 0 | 0 | 0 | 18 |
SUP | 100.00 (82.41-100.00) | 100.00 (82.41-100.00) | 100.00 (60.97-100.00) | 100.00 (75.75-100.00) | 100.00 (60.97-100.00) | 12 | 6 | 0 | 0 | 0 | 18 | ||
1000 | HAC | 100.00 (90.36-100.00) | 94.44 (81.86-98.46) | 90.48 (71.09-97.35) | 100.00 (79.61-100.00) | 100.00 (83.18-100.00) | 15 | 19 | 0 | 2 | 0 | 36 | |
SUP | 100.00 (93.36-100.00) | 96.30 (87.46-98.98) | 94.29 (81.39-98.42) | 100.00 (83.18-100.00) | 100.00 (89.57-100.00) | 19 | 33 | 0 | 2 | 0 | 54 |
