Table 2.

CpG probes differentially methylated by race in multivariable GLM analysis of all breast tumors

Gene/probeCpG IDGene descriptionMean βa AA (n = 216)Mean βa non-AA (n = 301)Delta βMean β normal breast (n = 9)CoefbAge-only–adjusted q valuecFully adjusted P valuedFully adjusted q valueeVariantChr
No overlapping variantf
 DSC2_E90_Fcg08156793Desmocollin 20.35640.26660.08980.15470.37776.48E−071.80E−063.31E−04None18
 KCNK4_E3_Fcg01352108Potassium channel, subfamily K, member 40.43180.35020.08160.28770.26444.07E−061.27E−049.60E−03None11
 GSTM1_P266_Fgcg19763514Glutathione S-transferase mu 10.57570.6269−0.05120.4544−0.26813.27E−023.23E−042.08E−02None1
 HBII-52_E142_Fcg24301180SNORD115-1/small nucleolar RNA, C/D box 115-10.40260.5402−0.13760.5768−0.52834.97E−123.30E−101.06E−07None15
Overlaps variant but minimal impact expectedh
 AXL_P223_Rcg09524393AXL receptor tyrosine kinase0.33110.24890.08220.10550.30156.15E−065.32E−043.11E−02SNP19
 DNAJC15_E26_Rcg10157207DnaJ (Hsp40) homolog, subfamily C, member 150.13990.1938−0.05390.1303−0.37892.30E−051.57E−051.68E−03SNP13
 TES_P182_Fcg00626984Testis-derived transcript (3 LIM domains)0.22230.2553−0.03300.1462−0.29898.61E−026.26E−043.50E−02SNP7
Overlaps variant and/or ancestral allelic differencei
 CCL3_P543_Rcg05481196Chemokine (C-C motif) ligand 30.89060.85980.03080.90810.30989.80E−033.76E−042.30E−02SNP17
 MAP2K6_E297_Fcg09190049Mitogen-activated protein kinase kinase 60.16510.11600.04910.10850.39672.30E−052.24E−032.24E−03SNP17
 DNAJC15_P65_Fcg05035143DnaJ (Hsp40) homolog, subfamily C, member 150.83180.8682−0.03640.8381−0.24492.49E−049.20E−044.94E−02SNP13
 ID1_P659_Rcg09569033Inhibitor of DNA-binding 1, dominant-negative helix-loop-helix protein0.18500.13360.05140.10400.43815.33E−041.68E−031.68E−03SNP20
 PADI4_P1158_Rcg19159961Peptidyl arginine deiminase, type IV0.47530.35890.11640.46710.34427.89E−119.24E−061.32E−03SNP1
 NTRK1_E74_Fcg18744444Neurotrophic tyrosine kinase, receptor, type 10.77430.60430.17000.74350.77922.08E−051.52E−051.68E−03SNP1
 NNAT_P544_Rcg10288563Neuronatin0.85040.8836−0.03320.8716−0.43243.24E−021.82E−051.80E−03SNP20
 WT1_P853_Fcg08219028Wilms tumor 10.18160.2852−0.10360.1518−0.58086.06E−052.96E−052.54E−03SNP11
 HLA-DQA2_P282_Rcg09782137Major histocompatibility complex, class II, DQ alpha 20.70650.7625−0.05600.7280−0.32964.73E−039.38E−057.55E−03SNP6
 ABCB4_P892_Fcg02810586ATP-binding cassette, sub-family B (MDR/TAP), member 40.67340.8491−0.17570.9052−0.92071.14E−155.33E−132.29E−10R, SNP7
 MSH3_P13_Rcg06210628mutS homolog 3 (E. coli)0.39980.6643−0.26450.5660−1.15111.75E−301.32E−271.70E−24Indel5
 MSH3_E3_Fcg14636131mutS homolog 3 (E. coli)0.53380.8121−0.27830.7250−1.41382.89E−275.40E−225.40E−22Indel5
 NOTCH1_P1198_Fcg26924342Notch 10.17610.13420.04190.15360.34961.32E−051.05E−062.71E−04R9
 ERCC1_P440_Rcg13282827Excision repair cross-complementing rodent repair deficiency, complementation group 10.17020.12370.04650.08170.34627.14E−071.80E−063.31E−04R19
 PTPRF_E178_Rcg09322748Protein tyrosine phosphatase, receptor type, F0.14290.1889−0.04600.1073−0.37151.71E−046.22E−061.00E−03R1
 ELL_P693_Fcg09597048Elongation factor RNA polymerase II0.39220.31170.08050.26120.29372.34E−051.95E−041.39E−02R19
 GML_E144_Fcg21475536Glycosylphosphatidylinositol anchored molecule like0.70430.7929−0.08860.7469−0.43653.63E−042.84E−041.92E−02Indel8

Multivariable GLM was conducted using, 1,287 CpG probes from the Illumina Cancer Panel I array in 517 breast tumors.

  • aMean of β values, which ranged from 0 (completely unmethylated) to 1 (fully methylated).

  • bCoefficients for comparison of AA cases to non-AA cases; positive coefficients indicate higher methylation in AA cases compared with non-AA cases, while negative values indicate higher methylation in non-AA cases than AA cases.

  • cAdjusted for age and multiple comparisons (FDR).

  • dAdjusted for age, menopausal status, stage, and intrinsic subtype.

  • eAdjusted for age, menopausal status, stage, intrinsic subtype, and multiple comparisons (Benjamini–Hochberg FDR).

  • fNo known variant overlaps CpG probe based on review of Ensembl, dbSNP, or as annotated in Byun et al. (19).

  • gGSTM1del variant occurring in the coding sequence shows allele frequency difference between AAs and whites of approximately 15% (38).

  • hProbe overlaps one SNP, but impact may be negligible due to location at end of probe, rarity of the minor allele, and/or no appreciable population difference (>10% in African vs. European) reported; therefore, probes were retained.

  • iProbes reported to overlap a SNP or repeat (R) according to Byun et al. (19), or based on updated information in Ensembl and dbSNP that are likely to disrupt probe binding.