Table 1.
Comparison of LOH Events Derived from SNiPDx and WGS Reference Data Set
| Variable | LOH detection by WGS |
|||
|---|---|---|---|---|
| All regions | ||||
| Two or more algorithms (605 LOH events)∗ |
Three-algorithm consensus (230 LOH events)† |
|||
| LOH | Non-LOH | LOH | Non-LOH | |
| LOH events by SNiPDx | ||||
| LOH | 202 | 22 | 93 | 2 |
| Non-LOH | 10 | 371 | 1 | 134 |
| Sensitivity, % | 95 | 99 | ||
| Specificity, % | 91 | 98 | ||
| κ Score (95% CI) | 0.89 (0.85–0.92) | 0.97 (0.94–1.00) | ||
| Variable | Diploid samples with no sub-clonal alterations (by WGS) |
|||
|---|---|---|---|---|
| Two or more algorithms (235 LOH events)∗ |
Three-algorithm consensus (116 LOH events)† |
|||
| LOH | Non-LOH | LOH | Non-LOH | |
| LOH events by SNiPDx | ||||
| LOH | 178 | 1 | 89 | 0 |
| Non-LOH | 5 | 51 | 1 | 26 |
| Sensitivity, % | 97 | 99 | ||
| Specificity, % | 99 | 100 | ||
| κ Score (95% CI) | 0.93 (0.87–0.98) | 0.98 (0.93–1.02) | ||
LOH, loss of heterozygosity; SNiPDx, SyNthetic lethal Interactions for Precision Diagnostics; WGS, whole genome sequencing.
∗
LOH gene calls defined when indicated by at least two WGS algorithms.
†
LOH calls in the subset of genes and samples where all three WGS algorithms agreed.