Table 2.

Methylation levels and frequencies above cutoff values in paired normal breast tissue adjacent to tumor, atypical ductal hyperplasia, ductal carcinoma in situ, and invasive ductal carcinoma

GenesNBAT (n = 12)ADH (n = 24)DCIS (n = 40)IDC (n = 45)P*
Multiple comparisonNBAT vs PATHNBAT vs ADHNBAT vs DCISNBAT vs IDCADH vs DCISADH vs IDCDCIS vs IDCPRE vs IDC
APC0 (0-0.04)3.04 (0-34.0)4.45 (0-416.71)43.64 (0.14-640.02)0.0030.00090.060.0070.020.310.080.210.12
1§ (8)8§ (33)15§ (38)24§ (53)0.0050.090.360.110.0090.680.030.0050.0009
CDH10 (0-3.19)0 (0-28.84)1.11 (0-10.09)6.39 (0.38-38.18)0.0020.0020.0080.020.020.230.140.050.09
1§ (8)7§ (29)12§ (31)21§ (47)0.010.100.210.190.030.880.070.0050.005
CTNNB10 (0-0)0 (0-0)0 (0-1.45)0.1 (0-3.14)0.160.030.300.790.050.350.070.050.05
1§ (8)4§ (17)6§ (15)11§ (47)0.380.420.590.600.210.960.310.240.15
ESR10 (0-15.2)0 (0-9.67)2.18 (0-16.22)0.7 (0-14.2)0.170.690.190.610.280.060.060.220.10
2§ (17)4§ (17)10§ (26)11§ (24)0.820.840.790.580.680.470.400.990.49
TIMP30 (0-11.44)1.65 (0-29.89)0.44 (0-13.48)2.33 (0-28.02)0.170.030.360.980.070.370.190.070.11
3§ (25)9§ (38)12§ (31)17§ (38)0.790.410.570.400.680.990.780.680.69
GSTPI0 (0-3.73)0 (0-0)0 (0-0.54)0 (0-1.46)0.280.130.680.130.210.120.220.330.27
2§ (17)3§ (12)7§ (18)11§ (24)0.540.910.670.730.590.360.230.700.24
  • *Upper P values refer to statistical analyses done using a hierarchical mixed model with unstructured covariance matrix; lower P values refer to statistical analysis done using a GEE logistic model.

  • Multiple comparison among NBAT, ADH, DCIS, and IDC. PATH merges the ADH, DCIS, and IDC groups (n = 138); PRE merges the ADH and DCIS groups (n = 76).

  • Median value (Interquartile Range, IQR).

  • §Number of samples methylated above cutoff value (% of methylated samples).