Inference of Tumor Phylogenies from Genomic Assays on Heterogeneous Samples

Table 2

Phylogenetic states of all components at all identified progression markers for the data of Navin et al. [14]. Columns show the states for the six inferred components (C1–C6). The additional normal component (C0) used to root the tree is included for completeness. “1” corresponds to an amplified region and “0” to nonamplified.

Marker ID	C0	C1	C2	C3	C4	C5	C6
1	0	1	0	1	1	1	0
2	0	1	0	1	1	1	0
3	0	0	0	1	0	0	0
4	0	0	0	1	0	0	0
5	0	0	0	1	1	1	0
6	0	0	0	0	1	0	1
7	0	0	0	0	1	0	1
8	0	0	0	1	0	0	0
9	0	1	0	1	0	1	0
10	0	1	0	1	1	1	0
11	0	1	0	1	1	1	0
12	0	1	0	1	1	1	0
13	0	0	0	0	1	1	0
14	0	0	1	0	1	0	0
15	0	0	0	0	0	0	1
16	0	1	0	0	1	0	0
17	0	0	0	0	1	0	0
18	0	0	0	0	1	0	1
19	0	0	0	0	1	1	1
20	0	0	0	0	1	1	1
21	0	0	0	0	1	1	1
22	0	0	1	0	0	0	0
23	0	0	1	0	0	0	0
24	0	1	0	0	0	0	1
25	0	0	0	1	1	1	0
26	0	0	0	1	1	1	0
27	0	0	0	1	1	1	0