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Table 3 Differences in methylation levels for each couple of frozen/FFPE DNA according to the three markers

From: Why do results conflict regarding the prognostic value of the methylation status in colon cancers? the role of the preservation method

Identity Levels of LINE-1methylation
(% of methylation)
Difference of methylation Levels of MLH1methylation
(% of methylation)
Difference of methylation Levels of MGMTmethylation
(% 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
  1. 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.
  2. *: 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.