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Table 2 Variants identified in DNA isolated from frozen cell line mixes

From: Quality control material for the detection of somatic mutations in fixed clinical specimens by next-generation sequencing

    

Cell Line / Sample Name

HCT116

MiaPaCa-2

H1975

SK-MEL-28

4-Cell Line Mix

Human Placenta

4-Cell Line Mix (Dil 1:2)

4-Cell Line Mix (Dil 1:3)

Gene Symbol

hg19 Coordinates

Variant Type

Variant

Freq. (%)

Found

Found

Found

Found

Expected

Found

Found

Expected

Found

Expected

Found

ABL1

133738370

SNV

G

 

52.4

N.A.

N.A.

N.A.

13.1

12.6 ± 0.5

N.A.

6.1

6.3 ± 0.2

4.1

4.4 ± 0.5

APC

112175770

SNV

A

 

98.1

74.4

51.7

88.5

78.1

80.0 ± 0.9

2.1

40.7

40.8 ± 0.9

27.8

29.4 ± 0.8

ATM

108138003

SNV

C

 

N.A.

N.A.

N.A.

N.A.

N.A.

N.A.

55.8

27.9

32.1 ± 0.2

37.2

40.6 ± 0.4

BRAF

140453136

SNV

A

 

N.A.

N.A.

N.A.

99.3

24.8

21.7 ± 4.0

N.A.

12.3

13.7 ± 0.2

8.2

9.6 ± 0.2

CDKN2A

21971153

SNV

T

 

N.A.

N.A.

96.4

N.A.

24.1

35.7 ± 2.6

N.A.

16.9

10.4 ± 1.1

11.3

8.4 ± 0.9

CSF1R

149433596

SNV

C

 

99.6

99.3

100.0

N.A.

74.7

58.6 ± 4.5

90.5

72.9

68.8 ± 0.6

78.8

80.5 ± 1.2

CSF1R

149433597

SNV

T

 

99.6

99.1

100.0

N.A.

74.7

62.3 ± 9.8

93.2

74.3

76.9 ± 0.7

80.6

85.7 ± 0.8

CTNNB1

41266134

DEL

CTT

 

50.2

N.A.

N.A.

N.A.

12.5

10.7 ± 1.8

N.A.

4.7

4.8 ± 0.6

3.2

3.1a ± 0.1

EGFR

55242487

SNV

T

 

N.A.

N.A.

N.A.

99.3

24.8

22.8 ± 2.6

N.A.

12.3

13.4 ± 0.1

8.2

8.0 ± 0.6

EGFR

55249063

SNV

A

 

100.0

23.2

70.6

100.0

73.4

75.3 ± 1.7

97.6

85.9

84.4 ± 0.7

89.8

90.1 ± 0.3

EGFR

55249071

SNV

T

 

N.A.

N.A.

70.7

N.A.

17.7

27.1 ± 2.5

N.A.

12.7

13.6 ± 1.1

8.4

8.9 ± 1.2

EGFR

55259515

SNV

G

 

N.A.

N.A.

56.7

N.A.

14.2

17.8 ± 0.7

N.A.

9.2

8.8 ± 1.3

6.1

6.4 ± 0.5

ERBB4

212812097

SNV

G

 

100.0

N.A.

75.9

N.A.

44.0

54.0 ± 0.2

62.9

58.4

46.8 ± 1.6

59.9

59.0 ± 2.3

FGFR3

1807894

SNV

A

 

100.0

100.0

99.6

100.0

99.9

99.6 ± 0.2

100.0

99.9

99.9 ± 0.1

99.9

99.8 ± 0.1

FLT3

28602367

SNV

A

 

46.9

N.A.

N.A.

N.A.

11.7

15.4 ± 3.2

N.A.

8.8

7.0 ± 0.3

5.9

6.4 ± 0.8

FLT3

28610183

SNV

C

 

100.0

66.5

99.6

69.2

83.8

80.9 ± 1.1

100.0

90.9

90.8 ± 0.1

93.9

93.4 ± 0.5

HRAS

534242

SNV

C

 

99.5

61.9

40.4

46.9

62.2

67.6 ± 1.1

2.6

34.7

32.0 ± 0.2

24.0

21.5 ± 1.2

KDR

55946354

SNV

A

 

48.5

N.A.

N.A.

N.A.

12.1

15.9 ± 1.0

51.3

33.3

34.5 ± 1.1

39.3

41.0 ± 1.1

KDR

55972974

SNV

T

 

52.6

N.A.

N.A.

N.A.

13.1

13.2 ± 4.3

N.A.

8.1

7.3 ± 0.5

5.4

5.1 ± 0.1

KRAS

25398281

SNV

A

 

46.4

N.A.

N.A.

N.A.

11.6

11.3 ± 0.7

N.A.

5.9

6.2 ± 0.4

3.9

4.2 ± 0.1

KRAS

25398285

SNV

T

 

N.A.

99.9

N.A.

N.A.

25.0

24.7 ± 1.2

N.A.

12.8

13.7 ± 0.5

8.5

9.5 ± 0.1

MET

116339672

SNV

T

 

N.A.

72.9

N.A.

N.A.

18.2

15.3 ± 2.0

N.A.

6.9

7.9 ± 0.0

4.6

4.8 ± 0.1

NOTCH1

139390822

SNV

G

 

N.A.

100.0

N.A.

N.A.

25.0

22.5 ± 0.3

N.A.

11.1

9.3 ± 0.2

7.4

7.1 ± 0.1

PDGFRA

55141055

SNV

G

 

99.7

100.0

99.7

100.0

99.8

99.9 ± 0.2

99.9

99.8

99.9 ± 0.1

99.8

100.0 ± 0.1

PDGFRA

55152040

SNV

T

 

N.A.

N.A.

50.8

N.A.

12.7

11.8 ± 2.8

3.8

8.8

7.5 ± 0.1

7.1

6.0 ± 0.7

PIK3CA

178917005

SNV

G

 

N.A.

N.A.

100.0

N.A.

25.0

28.6 ± 7.6

N.A.

11.6

13.9 ± 0.1

7.8

10.2 ± 0.6

PIK3CA

178927410

SNV

G

 

N.A.

N.A.

45.1

N.A.

11.3

10.7 ± 1.2

N.A.

5.8

5.9 ± 0.2

3.9

4.0 ± 0.2

PIK3CA

178952085

SNV

G

 

47.7

N.A.

N.A.

N.A.

11.9

11.3 ± 2.3

N.A.

4.9

6.4 ± 0.4

3.2

3.9a ± 0.1

PTEN

89711881

SNV

G

 

N.A.

N.A.

N.A.

99.3

24.8

24.3 ± 1.0

N.A.

11.8

9.5 ± 0.8

7.9

8.4 ± 0.6

RET

43613843

SNV

T

 

100.0

65.8

100.0

N.A.

66.4

70.8 ± 2.1

100.0

86.1

86.8 ± 0.6

90.7

91.3 ± 0.5

RET

43615612

SNV

G

 

45.2

N.A.

N.A.

N.A.

11.3

15.1 ± 0.3

N.A.

7.4

7.2 ± 0.3

5.0

2.9 ± 0.5

RET

43615633

SNV

G

 

N.A.

64.5

N.A.

N.A.

16.1

14.1 ± 0.0

N.A.

7.1

7.6 ± 0.5

4.7

3.7 ± 1.1

SMAD4

48586344

SNV

T

 

47.6

N.A.

N.A.

N.A.

11.9

17.2 ± 1.4

N.A.

8.1

6.5 ± 0.2

5.4

4.9 ± 0.2

SMARCB1

24176287

SNV

A

 

50.7

N.A.

40.8

N.A.

22.9

22.0 ± 2.3

N.A.

11.8

14.6 ± 0.1

7.9

10.7 ± 0.4

SMO

128846374

SNV

A

 

52.6

N.A.

N.A.

N.A.

13.1

10.5 ± 1.5

N.A.

5.8

7.8 ± 2.0

3.9

4.4 ± 0.2

TP53

7577025

SNV

T

 

N.A.

N.A.

N.A.

N.A.

N.A.

N.A.

79.0

39.5

29.1 ± 1.5

52.6

41.4 ± 1.1

TP53

7577120

SNV

A

 

N.A.

N.A.

99.9

N.A.

25.0

31.6 ± 2.6

N.A.

16.7

20.8 ± 0.8

11.1

16.0 ± 0.1

TP53

7577539

SNV

T

 

N.A.

99.5

N.A.

N.A.

24.9

18.8 ± 0.7

N.A.

9.6

11.3 ± 0.1

6.4

9.1 ± 0.1

TP53

7579472

SNV

G

 

94.2

N.A.

94.2

N.A.

47.1

63.6 ± 8.9

20.4

45.1

54.3 ± 2.3

36.9

42.7 ± 1.7

  1. Freq. Frequency; N.A., Not Applicable; a, these variants were called 90 % of the time