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Table 2 Topological ancestor–descendant and sibling relationship reconstruction on simulated data

From: Fast and scalable inference of multi-sample cancer lineages

Samples Cov Trees % SSNVs % AD % AD-Ord % AD-Corr % AD →Sib (−priv) % Sib %Sib-Corr % Sib →AD (−priv)
5 t-VAF 94 98.9 99 41.5 100 30.2 (2.6) 98.2 83.2 7.3 (1.5)
   98 99.5 99.5 40.4 100 26.3 99.2 84.8 6.6 (0.9)
  10K 95 98.8 98.7 40.4 99.9 30.5 (2.5) 97.8 82.5 7.7 (1.4)
   98 99.2 98.7 39 100 27.4 98.8 84.7 7 (1.3)
  1K 95 98.6 97.7 39.7 100.0 30.5 (2.3) 97.1 82.8 7.2 (1.3)
   98 99.4 99.5 38.1 99.7 29.2 98.9 83.9 7.5 (2.2)
  100 97 96.8 93.2 38.7 99.8 31.4 (3.5) 93.1 81.8 7.9 (1.7)
   97 97.3 94.8 35.2 99.7 30.1 95.3 83.7 7.2 (2.2)
10 t-VAF 97 97.5 96.2 58.8 100 43.1 (2.2) 96.9 94.4 3.3 (0.2)
   95 97.7 96.5 58.2 100 38.1 (1.9) 96.7 93.5 4.2 (1.4)
  10K 98 96.5 94.4 57.3 100 44.9 (4) 95.2 94 3.6 (0.4)
   96 97 96.1 56.5 100 39.8 (2.3) 96.2 93.3 4.3 (1.2)
  1K 98 97.4 96.4 57.5 99.9 45.2 (3.9) 96.8 94.1 3.7 (0.4)
   96 97 95.7 57.4 99.9 38.7 (2.4) 96 92.7 4.8 (1.5)
  100 93 90.8 75.7 52.3 99.7 38.6 (4.4) 78.0 93.9 3.4 (0.7)
   91 90.5 80.4 47.9 99.5 40.3 (5.7) 83.3 92.8 4.4 (1.5)
15 t-VAF 99 91.7 85 63.1 100 40.8 (2.2) 88 96.6 2 (0.2)
   96 92.1 87.5 61.7 100 41.5 (2) 89.1 96.9 2 (0.3)
  10K 98 92.3 85.3 61.2 100 44.3 (3.5) 87.6 96.2 2.4 (0.3)
   100 90.6 83.6 59.1 100 41.8 (2.6) 85.8 96.6 2.1 (0.3)
  1K 93 94.7 83.5 61.5 99.9 42.7 (4.3) 85.4 96.1 2.6 (0.6)
   100 91.8 85.4 59.1 100 43.5 (2.9) 87.8 96.7 2.1 (0.3)
  100 92 81.1 55.2 48.4 99.4 37.4 (5) 61.3 96.1 2.1 (0.3)
   98 81.8 57.1 46.1 99.8 36.5 (2.2) 63.1 96.2 2.2 (0.4)
  1. Results are shown for 5, 10, and 15 samples given true VAFs, 10,000 ×, 1,000 ×, and 100 × coverage data (without CNVs) obtained with localized (top row in each pair) and randomized (bottom row) sampling. All values are averaged over the number of reconstructed trees (Trees) out of 100 simulated trees. The following metrics are presented: SSNVs present in the tree (% SSNVs), ancestor–descendant pairs of mutations in the tree (AD), ordered AD pairs (AD-Ord), correctly ordered AD pairs (AD-Corr), unordered AD pairs reconstructed as siblings (AD →Sib) (with and without private mutation nodes), sibling pairs of mutations in the tree (Sib), correctly reconstructed sibling pairs (Sib-Corr), sibling pairs reconstructed as AD (Sib →AD) (with and without private mutation nodes). 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; t-VAF, true variant allele frequency; VAF, variant allele frequency.