Table 3

Differences in methylation levels for each couple of frozen/FFPE DNA according to the three markers

Identity

Levels of LINE-1 methylation

(% of methylation)

Difference of methylation

Levels of MLH1 methylation

(% of methylation)

Difference of methylation

Levels of MGMT methylation

(% of methylation)

Difference of methylation




DNA from cryo-preserved tissues

DNA from FFPE tissues

DNA from cryo-preserved tissues

DNA from FFPE tissues

DNA from cryo-preserved tissues

DNA from FFPE tissues


1

62.0

66.3

-4.3

51.5

57.7

-6.2

1.7

4.3

-2.6


2

66.1

67.2

-1.1

4.8

-

-

2.0

6.0

-4.0


3

64.6

64.8 †

-0.2

47.6

-

-

57.5

71.9 ‡

-14.3


4

57.2

52.3

5.0

6.8

-

-

55.8

49.3

6.5


5

61.6

64.2 †

-2.6

5.3

1,7*

3.6

1.9

6.2

-4.2


6

47.5

49.2

-1.7

2.9

3.9

-1.0

38.6

46.1

-7.5


7

59.4

56.6 †

2.9

5.1

1.9

3.3

59.4 †

43.4

16.0


8

47.9

46.5

1.3

3.4

1,5*

1.9

1.7

5.7

-4.0


9

64.5

61.2

3.3

33.1

13.3

19.7

14.7

18.2

-3.5


10

61.4

54.1

7.3

5.6

1.4

4.2

19.2

32.3

-13.1


11

60.5

50.1

10.4

3.9

3,4*

0.6

19.8

35.6 †

-15.8


12

60.2

62.2 †

-2.0

4.1

2.8

1.3

2.0

5.1

-3.2


13

45.1

62.5

-17.5

45.2

2.6

42.7

2.1

4.3

-2.2


14

57.0

60.8

-3.8

3.0

7,1*

-4.1

1.4

1.9

-0.5


15

59.2

63.2

-4.0

2.5

5.6

-3.1

1.4

4.9

-3.5


16

52.8

47.5 †

5.2

2.6

3,3*

-0.7

1.6

5.9

-4.3


17

61.0

55.6

5.3

77.7

4.6

73.1

1.7

30.2

-28.5


18

59.6

53.5

6.2

4.8

-

-

28.9

25.3

3.6


19

43.3

54.4

-11.2

2.2

-

73.9 †

62.2

11.7


20

61.7

57.6

4.1

4.6

3.5

1.1

15.7

25.2

-9.5


21

65.2

66.1 †

-1.0

6.1 †

-

-

2.2

7.0 ‡

-4.8


22

50.9

49.1 †

1.8

3.5

3.3

0.3

1.9

6.8

-5.0


23

61.6

59.4

2.2

3.5

2.1

1.4

1.6

4.6

-2.9


24

59.3

58.0

1.4

2.4

3.5

-1.1

20.8

32.4

-11.7


25

61.7

71.0

-9.3

4.1

-

-

31.7

1,9*

29.8


26

56.7

52.2

4.4

2.4

0.9

1.5

52.8 †

20.4

32.4


27

45.5 ‡

44.3

1.3

-

5.9

-

-

4.2

-


28

65.3

57.4

7.9

6.6

2,7*

3.9

41.8

25.2 ‡

16.6


29

64.0

57.3

6.7

3.4

2,4*

1.0

2.2

3.3

-1.1


30

56.4

56.7

-0.3

11.5

7.3

4.3

3.9

5.3

-1.5


31

62.0

62.9

-1.0

32.8

-

-

5.7

5.3

0.4


32

67.2

62.0

5.2

3.9

5.2

-1.2

19.0

51.8

-32.8


33

60.2

62.4 †

-2.3

4.0

3.9

0.1

2.0

7.9

-5.9


34

62.0

61.7

0.3

3.6

-

-

2.2

5.9

-3.7


35

56.9

53.3

3.5

3.8

-

-

2.1

5.6

-3.5


36

40.5

41.1

-0.6

3.0

3.6

-0.6

1.7

5.2

-3.5


37

59.0

62.1 †

-3.0

2.7

3.3

-0.6

88.3 †

73.1 ‡

15.1


38

62.3

58.5 †

3.8

4.3

1.5

2.8

68.2

71.7

-3.5


39

50.4

53.2

-2.9

4.8

4.5

0.3

1.9

4.6

-2.7


40

36.2

34.7

1.5

3.1

-

-

2.0

5.9

-4.0


Values of methylation levels correspond to the average level of methylation of the three CpG sites evaluated for LINE-1 and the five CpG sites evaluated for MLH1 and MGMT. Data were collected using the pyrogram which had the best internal control of conversion.

*: indicates an uncertain result due to the low intensity of the pyrogram. †: indicates an uncertain conversion (5.0 to 7.0% of unconverted cytosines). ‡: indicates a poor conversion (more than 7.0% of unconverted cytosines). Numbers in bold indicate a difference of methylation level outside the -6.0/+6.0% interval. Differences in methylation levels were calculated by subtracting the level of methylation of the cryo-preserved sample from the level of methylation of the FFPE sample.

Tournier et al. BMC Cancer 2012 12:12   doi:10.1186/1471-2407-12-12

Open Data