Table 3.
Comparison of Alteration Events in Samples with Biallelic Loss of ATM, Derived from SNiPDx and oNGS
| Variable | LOH detection by oNGS |
|||||||
|---|---|---|---|---|---|---|---|---|
| Biallelic LOF |
Mutation status (SNVs + InDels) |
LOH status |
HomDel status |
|||||
| Biallelic | Not biallelic | Mutant | WT | LOH | Non-LOH | HomDel | Not HomDel | |
| Calls by SNiPDx | ||||||||
| Detected | 13 | 0 | 8 | 0 | 16 | 1 | 5 | 0 |
| Not detected | 1 | 13 | 0 | 19 | 0 | 10 | 1 | 17 |
| Sensitivity, % | 93 | 100 | 100 | 83 | ||||
| κ Score (95% CI) | 0.93 (0.79–1.07) | 1 | 0.92 (0.77–1.08) | 0.88 (0.65–1.11) | ||||
ATM, ataxia-telangiectasia mutated; HomDel, homozygous deletion; InDel, insertion/deletion; LOF, loss of function; LOH, loss of heterozygosity; oNGS, orthogonal next-generation sequencing; SNiPDx, SyNthetic lethal Interactions for Precision Diagnostics; SNV, single-nucleotide variant; WT, wild type.