Table 2 Comparison of absolute ERBB2 copy number estimation by fluorescence in situ hybridization (FISH) and cancer panel next generation sequencing (NGS) in breast cancers.

From: Deriving tumor purity from cancer next generation sequencing data: applications for quantitative ERBB2 (HER2) copy number analysis and germline inference of BRCA1 and BRCA2 mutations

Tumor purity (NGS)

ERBB2 copies (FISH)

CEP17 copies (FISH)

ERBB2 / CEP17 ratio (FISH)

ERBB2 copies (NGS)

NF1 copies (NGS)

ERBB2 / NF1 ratio (NGS)

ERBB2 interpretation (FISH)

ERBB2 interpretation (NGS)

49%

32.90

1.50

21.93

60.87

3.54

17.19

Positive

Positive

59%

29.73

1.63

18.24

43.89

1.93

22.74

Positive

Positive

60%

16.87

1.67

10.10

21.71

2.31

9.40

Positive

Positive

47%

20.10

2.23

9.01

30.18

1.83

16.49

Positive

Positive

53%

29.03

3.33

8.72

29.05

1.40

20.75

Positive

Positive

49%

12.90

1.93

6.68

15.65

2.22

7.05

Positive

Positive

15%

16.30

2.47

6.60

31.43

3.08

10.20

Positive

Positive

64%

13.33

2.87

4.65

8.80

2.03

4.33

Positive

Positive

47%

13.83

4.23

3.27

15.78

5.98

2.64

Positive

Positive

72%

5.68

1.74

3.26

8.73

2.08

4.20

Positive

Positive

40%

6.90

2.80

2.46

14.98

3.75

3.99

Positive

Positive

69%

6.70

3.23

2.07

2.00

2.14

0.93

Positive

Negative

33%

4.50

2.37

1.90

4.75

3.99

1.19

Negative

Negative

52%

2.40

1.90

1.26

2.54

2.05

1.24

Negative

Negative

80%

1.80

1.43

1.26

1.12

1.07

1.05

Negative

Negative

81%

3.03

2.60

1.17

1.36

2.35

0.58

Negative

Negative

69%

2.03

1.77

1.15

2.23

1.94

1.15

Negative

Negative

77%

3.07

2.73

1.12

2.91

3.08

0.94

Negative

Negative

46%

2.10

1.90

1.11

2.96

1.94

1.53

Negative

Negative

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