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-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.

Popova et al. Genome Biology 2009 10:R128   doi:10.1186/gb-2009-10-11-r128

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