Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays

Table 1 Experimental and in silico DNA indexes and parameters of GAP model

Sample ID	DNA index FCM	DNA index GAP	DNA index OverUnder	Tumor content 1-p_BAF	Contraction q_LRR
BLC_B1_T14	1.14	0.85	0.98	0.85	0.37
BLC_B1_T17	0.84	0.82	0.97	0.77	0.17
BLC_B1_T19	1.6	1.63	2.93	0.4	0.27
BLC_B1_T20	1.41	1.48	3.06	0.4	0.2
BLC_B1_T22^a	1.98	0.94	1.02	0.87	0.44
BLC_T07	1.68	1.49	3.12	0.44	0.28
BLC_T09	2.02	1.85	1.89	0.92	0.47
BLC_T10	1.88	1.9	1.07	0.95	0.47
BLC_T12	1.51	1.54	2.56	0.65	0.35
BLC_T15	1.11	0.89	0.99	0.74	0.27
BLC_T23	1.32	1.39	2.72	0.41	0.21
BLC_T31	1.91	1.84	1.48	0.84	0.45
BLC_T34^a	1.55	0.99	1.04	0.87	0.42
BLC_T37	1.51	1.53	1.44	0.89	0.44
L_B1_T24B	1.84	1.64	2.61	0.59	0.29
L_B1_T25A	1.00	1.04	3.03	0.39	0.17
L_B1_T30	1.84	1.83	1.53	0.78	0.42
L_B1_T47	1.00	1.03	1.47	0.45	0.17

^aTwo samples with clear near-diploid pattern of GAP and discordant experimental DNA indexes.

ISSN: 1474-760X