OncoNEM: inferring tumor evolution from single-cell sequencing data

Table 1 Comparison of origin of mutations inferred by OncoNEM with origins inferred by Li et al.

		1	2	3	4	5, 7	6	10	11, 12	13
A	NIPBL	*0.33*	*0.33*	*0.33*	0.00	0.00	0.00	0.00	0.00	0.00
	CFTR	0.45	0.45	0.09	0.00	0.00	0.00	0.00	0.00	0.00
	DHX57	0.45	0.45	0.09	0.00	0.00	0.00	0.00	0.00	0.00
	ASTN1	0.25	0.25	0.51	0.00	0.00	0.00	0.00	0.00	0.00
B	ATM	0.00	0.00	0.00	1.00	0.00	0.00	0.00	0.00	0.00
C	COL6A3	0.07	0.07	0.07	0.00	0.00	0.00	0.76	0.01	0.00
	KIAA1958 ¹	0.00	0.00	0.00	0.00	0.00	0.00	0.98	0.00	0.00
	KIAA1958 ²	0.19	0.19	0.19	0.02	0.00	0.02	0.38	0.00	0.00

Posterior probabilities of θ inferred by OncoNEM for the eight recurrently mutated genes analyzed by Li et al. A, B and C denote the clones inferred by Li et al., and 1 to 14 denote the clones inferred by OncoNEM. Visual comparison of the OncoNEM tree with the phylogeny inferred by Li et al. suggests that clone A corresponds to clones 1–3, clone B corresponds to clones 4–7 and clone C corresponds to clones 10–13 (indicated in bold). Overall, both methods assign mutations to the same clones. KIAA1958 ¹ denotes mutation at chromosome 9, position 114376732. KIAA1958 ² denotes mutation at chromosome 9, position 114376902

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