Table 3 |
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|
Self-consistency of copy numbers and LOH in dilution series by using GAP and OverUnder analyses |
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|
GAP |
CN |
LOH |
DNA index |
Tumor DNA |
1-p BAF |
q LRR |
||
|
|
||||||||
|
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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|
Popova et al. Genome Biology 2009 10:R128 doi:10.1186/gb-2009-10-11-r128 |
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