|
DNA region
|
Controla
|
Adjacentb
|
Invasivec
|
Adjacent vs. control
|
Invasive vs. control
|
Invasive vs. adjacent
|
|---|
| |
N
|
Mean
|
SD
|
N
|
Mean
|
SD
|
N
|
Mean
|
SD
|
Diff.
|
P-valued
|
Diff.
|
P-valued
|
Diff.
|
P-valuee
|
|---|
|
Promoter region
| | | | | | | | | | | | | | | |
|
BRCA1
|
15
|
1.6
|
1.1
|
105
|
1.4
|
4.3
|
105
|
3.0
|
9.6
|
-0.2
|
NS
|
1.4
|
NS
|
1.6
|
0.031
|
|
CD44f
|
18
|
1.6
|
0.6
|
37
|
1.8
|
0.9
|
37
|
2.6
|
2.7
|
0.2
|
NS
|
1.0
|
NS
|
0.8
|
NS
|
|
ESR1f
|
18
|
5.9
|
3.1
|
37
|
7.9
|
6.0
|
37
|
6.7
|
7.8
|
2.0
|
NS
|
0.8
|
NS
|
-1.2
|
NS
|
|
GSTM2
|
16
|
1.8
|
2.0
|
107
|
3.0
|
6.1
|
107
|
19.3
|
22.9
|
1.2
|
NS
|
17.5
|
0.004
|
16.3
|
<0.0001
|
|
GSTP1
|
17
|
2.5
|
2.0
|
118
|
1.6
|
3.7
|
118
|
9.9
|
16.8
|
-0.9
|
NS
|
7.4
|
NS
|
8.3
|
<0.0001
|
|
MAGEA1f
|
17
|
84.8
|
4.9
|
32
|
84.2
|
4.8
|
37
|
67.0
|
16.2
|
-0.6
|
NS
|
-17.8
|
0.0001
|
-17.2
|
<0.0001
|
|
MSI1f
|
18
|
3.8
|
2.1
|
36
|
4.2
|
2.5
|
37
|
9.2
|
7.4
|
0.4
|
NS
|
5.3
|
0.0001
|
5.0
|
0.0003
|
|
NFE2L3f
|
17
|
28.9
|
14.7
|
36
|
26.9
|
13.7
|
37
|
33.7
|
24.4
|
-2.0
|
NS
|
4.8
|
NS
|
6.8
|
NS
|
|
RASSF1A
|
18
|
2.8
|
2.2
|
124
|
9.7
|
10.7
|
124
|
33.3
|
23.4
|
6.9
|
<0.0001
|
30.5
|
<0.0001
|
23.6
|
<0.0001
|
|
RUNX3
|
17
|
3.3
|
1.2
|
119
|
4.0
|
3.3
|
119
|
11.4
|
12.7
|
0.7
|
NS
|
8.1
|
0.061
|
7.4
|
<0.0001
|
|
SIX3
|
17
|
5.8
|
2.8
|
115
|
5.3
|
4.0
|
115
|
15.7
|
14.9
|
-0.5
|
NS
|
9.9
|
0.026
|
10.4
|
<0.0001
|
|
TFF1
|
18
|
81.8
|
5.4
|
122
|
72.0
|
16.9
|
122
|
49.2
|
22.3
|
-9.8
|
0.008
|
-32.6
|
<0.0001
|
-22.8
|
<0.0001
|
|
Upstream of promoter
| | | | | | | | | | | | | | | |
|
EN1
|
18
|
17.8
|
5.3
|
122
|
20.0
|
10.2
|
122
|
32.9
|
15.3
|
2.2
|
NS
|
15.1
|
<0.0001
|
12.9
|
<0.0001
|
|
PAX3
|
17
|
2.9
|
1.2
|
121
|
4.0
|
5.2
|
121
|
10.8
|
11.1
|
1.1
|
NS
|
7.9
|
0.0003
|
6.8
|
<0.0001
|
|
PITX2f
|
17
|
26.5
|
6.1
|
35
|
27.6
|
8.6
|
36
|
36.1
|
11.3
|
1.1
|
NS
|
9.6
|
0.001
|
8.5
|
<0.0001
|
|
SGK1
|
18
|
1.6
|
1.2
|
124
|
3.9
|
3.7
|
124
|
13.0
|
12.2
|
2.3
|
<0.0001
|
11.4
|
<0.0001
|
9.1
|
<0.0001
|
|
Introns
| | | | | | | | | | | | | | | |
|
APC
|
18
|
2.0
|
1.9
|
114
|
2.9
|
8.3
|
114
|
14.8
|
19.6
|
0.9
|
NS
|
12.8
|
0.058
|
11.9
|
<0.0001
|
|
EGFR
|
18
|
4.5
|
1.3
|
126
|
7.3
|
5.2
|
126
|
19.4
|
14.8
|
2.8
|
0.006
|
14.9
|
<0.0001
|
12.1
|
<0.0001
|
|
LHX2f
|
18
|
21.1
|
5.3
|
36
|
25.8
|
13.1
|
37
|
36.1
|
12.6
|
4.7
|
NS
|
15.0
|
<0.0001
|
10.3
|
0.0007
|
|
RFX1
|
18
|
18.0
|
5.3
|
126
|
19.3
|
9.7
|
126
|
39.4
|
13.1
|
1.3
|
NS
|
21.4
|
<0.0001
|
20.1
|
<0.0001
|
|
SOX9
|
18
|
8.4
|
4.3
|
123
|
9.1
|
7.4
|
123
|
15.2
|
14.3
|
0.7
|
NS
|
6.8
|
NS
|
6.1
|
0.002
|
|
DNA Repeats
| | | | | | | | | | | | | | | |
|
LINE-1
|
18
|
68.7
|
1.4
|
129
|
72.8
|
2.6
|
129
|
71.2
|
4.3
|
4.1
|
<0.0001
|
2.5
|
0.0003
|
-1.6
|
0.001
|
|
Sat2
|
18
|
52.6
|
8.0
|
128
|
57.4
|
12.7
|
128
|
52.0
|
13.4
|
4.8
|
0.002
|
-0.6
|
NS
|
-5.4
|
<0.0001
|
-
aReduction mammoplasty samples from women unaffected with breast cancer
-
bSamples from histologically normal tissue adjacent to the tumor
-
cSamples from the cancer component of the tumor
-
dFrom an independent sample Wilcoxon Rank Sum test comparing control mammoplasty vs. adjacent samples
-
eFrom a dependent sample Wilcoxon Sign Rank test. P-values > 0.10 are suppressed. Diff, difference in mean methylation; SD, standard deviation
-
fThese seven assays were not pursued beyond the pilot phase and, therefore, had 32-37 paired cancer and adjacent samples instead of 105-129
- Differences were determined to be statistically significant at p < 0.001 for the complete sample set and p < 0.01 for regions only examined in the pilot study
