Table 3.
Topological ancestor–descendant and sibling relationship reconstruction on simulated data in the presence of copy number variants
| Samples | Trees | % SSNVs | % AD | % AD-Ord | % AD-Corr | % AD →Sib (−priv) | % Sib | % Sib-Corr | % Sib →AD (−priv) |
|---|---|---|---|---|---|---|---|---|---|
| 5 | 95 | 96.2 | 89.1 | 14.4 | 93.7 | 20 (0.4) | 92.6 | 80.8 | 2.4 (0) |
| 98 | 97.42 | 91.96 | 10.74 | 96.1 | 0.20 | 94.85 | 80.46 | 2 (0.02) | |
| 10 | 91 | 94.8 | 77.1 | 14.6 | 93.5 | 24.9 (0.6) | 90.9 | 91.8 | 1.3 (0) |
| 92 | 94.55 | 78.97 | 11.95 | 93.1 | 0.41 | 90.5 | 91.7 | 1.1 (0.01) | |
| 15 | 97 | 91.8 | 65.9 | 11.1 | 92.5 | 23.3 (0.4) | 85.5 | 94.6 | 0.7 (0) |
| 94 | 92.9 | 69.6 | 10.8 | 94.5 | 24.2 (0.35) | 87.5 | 94.8 | 0.6 (0.01) |
Results are shown for 5, 10, and 15 samples given 1,000 × coverage data obtained with localized (top row in each pair) and randomized (bottom row) sampling with approximately 80% of SSNVs in CNV regions. All values are averaged over the number of reconstructed trees. AD, ancestor–descendant; CNV, copy number variant; Corr, correctly ordered; Cov, coverage; Ord, ordered; priv, private mutation nodes; Sib, sibling; SSNV, somatic single nucleotide variant.