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Table 3 Mean percent methylation by gene and tissue type from the Breast Cancer Care in Chicago study

From: Exploring DNA methylation changes in promoter, intragenic, and intergenic regions as early and late events in breast cancer formation

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
  1. aReduction mammoplasty samples from women unaffected with breast cancer
  2. bSamples from histologically normal tissue adjacent to the tumor
  3. cSamples from the cancer component of the tumor
  4. dFrom an independent sample Wilcoxon Rank Sum test comparing control mammoplasty vs. adjacent samples
  5. eFrom a dependent sample Wilcoxon Sign Rank test. P-values > 0.10 are suppressed. Diff, difference in mean methylation; SD, standard deviation
  6. fThese seven assays were not pursued beyond the pilot phase and, therefore, had 32-37 paired cancer and adjacent samples instead of 105-129
  7. 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