Fast and scalable inference of multi-sample cancer lineages

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

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)

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.

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