| |
All samples
| |
ER/PR Positive
| |
ER/PR Negative
| |
|---|
|
Na
|
Diff.b
|
95 % CIc
|
P-Valued
|
Na
|
Diff.b
|
95 % CIc
|
P-Valued
|
Na
|
Diff.b
|
95 % CIc
|
P-Valued
|
|---|
|
Promoter regions
| | | | | | | | | | | | |
|
BRCA1
|
198
|
1.7
|
(0, 4)
|
NS
|
136
|
1
|
(-1, 4)
|
NS
|
62
|
3
|
(0, 8)
|
0.09
|
|
CD44e
|
54
|
0.5
|
(0, 1)
|
NS
|
32
|
0
|
(-0.4, 1)
|
NS
|
22
|
0
|
(0,2)
|
NS
|
|
ESR1e
|
54
|
-1.5
|
(-3, 0)
|
0.099
|
32
|
-1
|
(-4, 1)
|
NS
|
22
|
-2
|
(-4, 1)
|
NS
|
|
GSTM2
|
212
|
16.8
|
(13, 21)
|
< 0.0001
|
146
|
10
|
(6, 16)
|
< 0.0001
|
66
|
32
|
(24, 38)
|
< 0.0001
|
|
GSTP1
|
227
|
8.3
|
(6, 12)
|
< 0.0001
|
159
|
9
|
(6, 14)
|
< 0.0001
|
68
|
6
|
(2, 12)
|
0.016
|
|
MAGEA1e
|
54
|
-14.5
|
(-22, -9)
|
< 0.0001
|
32
|
-22
|
(-30, -14)
|
< 0.0001
|
22
|
-4
|
(-12, 3)
|
NS
|
|
MSI1e
|
54
|
4.7
|
(2, 8)
|
0.005
|
32
|
4
|
(1, 10)
|
0.057
|
22
|
5
|
(1, 9)
|
0.01
|
|
NFE2L3e
|
54
|
5.6
|
(-4, 16)
|
NS
|
32
|
19
|
(9, 31)
|
0.001
|
22
|
-15
|
(-26, -4)
|
0.01
|
|
RASSF1A
|
234
|
23.5
|
(19, 28)
|
< 0.0001
|
160
|
26
|
(21, 31)
|
< 0.0001
|
74
|
18
|
(12, 25)
|
< 0.0001
|
|
RUNX3
|
227
|
6.6
|
(4, 9)
|
< 0.0001
|
156
|
9
|
(6, 11)
|
< 0.0001
|
71
|
2
|
(-1, 7)
|
NS
|
|
SIX3
|
221
|
10.9
|
(9, 14)
|
< 0.0001
|
151
|
10
|
(7, 14)
|
< 0.0001
|
70
|
13
|
(8, 19)
|
< 0.0001
|
|
TFF1
|
230
|
-21.6
|
(-26, -17)
|
< 0.0001
|
159
|
-25
|
(-30, -19)
|
< 0.0001
|
71
|
-14
|
(-23, -5)
|
0.002
|
|
Upstream of promoter
| | | | | | | | | | | | |
|
EN1
|
230
|
13.1
|
(10, 17)
|
< 0.0001
|
158
|
12
|
(8, 16)
|
< 0.0001
|
72
|
16
|
(9, 24)
|
< 0.0001
|
|
PAX3
|
230
|
7.3
|
(5, 10)
|
< 0.0001
|
159
|
6
|
(4, 9)
|
< 0.0001
|
71
|
10
|
(6, 15)
|
< 0.0001
|
|
PITX2e
|
54
|
7.8
|
(4, 11)
|
< 0.0001
|
32
|
7
|
(3, 10)
|
< 0.0001
|
22
|
10
|
(1, 16)
|
0.026
|
|
SGK1
|
233
|
9.8
|
(8, 12)
|
< 0.0001
|
160
|
9
|
(7, 12)
|
< 0.0001
|
73
|
11
|
(7, 16)
|
< 0.0001
|
|
Introns
| | | | | | | | | | | | |
|
APC
|
221
|
12.3
|
(9, 16)
|
< 0.0001
|
153
|
12
|
(8, 16)
|
< 0.0001
|
68
|
15
|
(9, 22)
|
< 0.0001
|
|
EGFR
|
235
|
12
|
(9, 15)
|
< 0.0001
|
161
|
15
|
(11, 18)
|
< 0.0001
|
74
|
6
|
(2, 11)
|
0.009
|
|
LHX2e
|
54
|
8.1
|
(2, 15)
|
0.017
|
32
|
8
|
(3, 13)
|
0.006
|
22
|
9
|
(-5, 22)
|
NS
|
|
RFX1
|
235
|
19.8
|
(17, 23)
|
< 0.0001
|
161
|
20
|
(16, 23)
|
< 0.0001
|
74
|
21
|
(16, 26)
|
< 0.0001
|
|
SOX9
|
231
|
6.2
|
(3, 9)
|
< 0.0001
|
158
|
6
|
(3, 10)
|
< 0.0001
|
73
|
6
|
(1, 13)
|
0.031
|
|
DNA Repeats
| | | | | | | | | | | | |
|
LINE-1
|
238
|
-1.5
|
(-2, -1)
|
< 0.0001
|
162
|
-2
|
(-3, -1)
|
< 0.0001
|
76
|
-1
|
(-3, 0)
|
0.074
|
|
Sat2
|
237
|
-5.4
|
(-9, -2)
|
0.001
|
161
|
-6
|
(-10, -2)
|
0.003
|
76
|
-5
|
(-10, 1)
|
0.109
|
-
aNumber of samples analyzed; the small differences in numbers of samples in this table compared to Table 3 are due to missing data on ER/PR status
-
bDifference in mean percent methylation (cancer and adjacent) was estimated via linear regression model with generalized estimating equations to account for within-patient covariance
-
cBias corrected, bootstrapped 95 % confidence intervals (CI) were estimated via 1000 bootstrap replications to account for skewed methylation distributions
-
dApproximate p-value estimated from a Wald test of the normal-based bootstrapped estimate over its standard error. P-values > 0.1 are suppressed
-
eThese seven assays were not pursued beyond the pilot phase and therefore have considerably fewer cancer and adjacent tissue samples analyzed
- All estimates of mean percent methylation are adjusted for age, race/ethnicity, stage at diagnosis, tumor grade, and either adjusted for or stratified by ER/PR status
