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

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

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   
  1. 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.