Table 3 Verification analysis of selected somatic single-nucleotide mutation (SSM) calls, stratified by confidence category. Only one of 85 SSM calls, targeted for verification, could be confirmed. WGS = whole genome sequencing.
Verification result of variant allele | high-confidence (N = 28) | medium-confidence (N = 29) | low-confidence (N = 28) | Interpretation of original WGS call |
|---|---|---|---|---|
found in target tissue (subject-specific) | 1 | 0 | 0 | correct |
found in target and reference tissue (subject-specific or non-specific) | 5 | 1 | 4 | mosaicism (if subject-specific verification); allele-specific sequencing bias |
fully present in target and reference tissue (≈50 or 100%) | 0 | 1 | 9 | single nucleotide polymorphism |
unlikely or unclearly present (e.g. few high-quality reads) | 1 | 6 | 3 | position difficult to call |
missing in target and reference tissue | 21 | 21 | 12 | sequencing or mapping inaccuracies |
