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

Table 3 Self-consistency of copy numbers and LOH in dilution series by using GAP and OverUnder analyses

GAP	CN	LOH			DNA index	Tumor DNA	1-pBAF	qLRR
CRL2324	1	1			1.45	1	1	0.45
CRL2324_79	0.93	0.98			1.46	0.79	0.8	0.35
CRL2324_50	0.9	0.97			1.44	0.5	0.42	0.22
CRL2324_47	0.78	0.96			1.49	0.47	0.42	0.24
CRL2324_45	0.81	0.96			1.5	0.45	0.35	0.18
CRL2324_34	0.69	0.93			1.53	0.34	0.27	0.16
CRL2324_30	0.73	0.93			1.52	0.3	0.25	0.12
CRL2324_23	0.72	0.93			1.59	0.23	0.26	0.14
CRL2324_21	0.7	0.92			1.64	0.21	0.14	0.12
OverUnder	CN	LOH	CN ± 1	CN CBS	DNA index	Tumor DNA
CRL2324	1	1	1	1	2.48	1
CRL2324_79	0.36	0.94	0.74	0.46	2.16	0.79
CRL2324_50	0.21	0.45	0.65	0.1	2.64	0.5
CRL2324_47	0.22	0.45	0.68	0.1	2.5	0.47
CRL2324_45	0.34	0.45	0.71	0.11	2.85	0.45
CRL2324_34	0.24	0.44	0.56	0.19	2.57	0.34
CRL2324_30	0.14	0.45	0.48	0.23	2.54	0.3
CRL2324_23	0.31	0.45	0.68	0.23	2.51	0.23
CRL2324_21	0.07	0.47	0.12	0.05	1.11	0.21

CN = copy number; LOH = loss of heterozygosity; tumor DNA = proportion of tumor DNA in the dilution; DNA index = in silico DNA index with each algorithm; 1-p BAF and q LRR are parameters of the model GAP; CN ± 1, copy numbers are considered to be consistent when the difference is less than or equal to 1; CN CBS, consistency is calculated on averaged (by median) and rounded copy-number assignments in CBS determined segments.

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