Inference of Tumor Phylogenies from Genomic Assays on Heterogeneous Samples

Table 1

Marker regions determined to be significantly amplified across components for the data of Navin et al. [14]. The table provides, for each marker region, a unique identifier, cytogenetic coordinates, probe positions along the genomic axis, and gene IDs for genes identified as having some known association with cancers.

Marker ID	Cytogenetic coordinates	Chromosome positions	Annotated cancer-related genes
1	1q32.1-1q32.2	196117366-206330147	CD55, MDM4, NR5A2,PTPN7, IL10, CNTN2,CD34
2	1q44	242649493-245131380	SMYD3
3	2p12	76777788-78642108	None
4	3q25.1-3q25.2	151037467-154216571	None
5	5p15.33-5p14.2	3485419-24119655	PAPD7, TAG, CDH18
6	5q21.1-5q21.3	100224934-106834646	None
7	5q22.3-5q23.1	115172420-118711133	TNFAIP8, ATG12, SEMA6A
8	7q31.2-7q31.31	116016939-120372452	ING3,ASZ1, WNT2, ST7
9	8q12.1	55969808-58018737	None
10	8q12.3-8q13.2	63931435-69387571	MYBL1
11	8q13.2-8q13.3	69634776-74092165	TRPA1
12	8q21.11-8q24.3	77351432-143296089	MYC
13	11q13.2-11q13.4	67830873 -70354248	CCND1, CTTN, FGF4, FGF3
14	11q14.1-11q13.4	74383378-82935709	None
15	11q23.3	115171785-116542726	None
16	12p11.22-12p11.21	28901065-33207415	ERGIC2
17	15q25.2-15q25.3	82525637-85513682	None
18	15q26.3	96434691-99661839	None
19	17q11.2	23392447-25127504	RAB34, NEK8, TRAF4, FOXN1
20	17q12-17q21.2	32705491-37628927	STAT5, ERBB2, GRB7
21	17q21.33	45403785-47282174	SPAG9, UTP18, CA10, ANKRD40, CACNA1G, PPP1R9B
22	18q21.32-18q22.2	56806538-66527883	TNFRSF11A, BCL2, SERPINB5, SERPINB13, SERPINB4, SERPINB3, CDH19
23	18q22.2-18q22.3	66607283-71314138	None
24	19q12	34017456-36812510	CCNE1
25	20q13.12	44249187-45563781	None
26	20q13.2-20q13.32	50440150-57022263	ZNF217, CYP24A1, BCAS1, AURKA, CTCFL, ZBP1, RAB22A, GNAS, SDX16
27	20q13.33	57624055-58571221	None