Table 3.

TCGA validation of differential breast tumor methylation in genes showing racial variation in the CBCS

450K probeChrGeneGoldenGate probeDistance b/w GG and TCGA probes (bp)aMean β AAMean β non-AAPb
cg1056449819AXLAXL_P223_R530.2230.1820.05
cg0324704919AXLAXL_E61_F140.0860.0630.22
cg1272246919AXLAXL_E61_F1690.1890.1470.12
cg0503514313DNAJC15DNAJC15_P65_F00.0860.8180.002
cg12504148c13DNAJC15DNAJC15_P65_F340.6100.6900.02
cg1472996213DNAJC15DNAJC15_E26_R1770.1510.2220.02
cg0056675918DSC2DSC2_E90_F580.0650.0550.34
cg1387099018DSC2DSC2_E90_F1210.2070.2070.99
cg0019667118DSC2DSC2_E90_F−580.0620.0600.87
cg116800551GSTM1GSTM1_P266_F760.4100.4900.04
cg2427576918IMPACTIMPACT_P234_R−20.1370.1080.18
cg1398135618IMPACTIMPACT_P234_R−780.2050.1960.69
cg0340043718IMPACTIMPACT_P234_R70.0590.0360.21
cg2275744718IMPACTIMPACT_P234_R−1320.1700.1480.45
cg0135210811KCNK4KCNK4_E3_F00.3290.2810.05
cg0939619611KCNK4KCNK4_E3_F1760.1040.0460.06
cg0612949811KCNK4KCNK4_E3_F590.1690.1420.09
cg1467325611KCNK4KCNK4_E3_F1790.1050.0460.04
cg028305763RAF1RAF1_P330_F00.2550.2460.40
cg185687143RAF1RAF1_P330_F−20.0720.0610.27
cg137030213RAF1RAF1_P330_F1570.1460.1250.21
cg112979343RAF1RAF1_P330_F−1390.0200.0180.12
cg245065333RAF1RAF1_P330_F−1220.0220.0220.93
cg230329653RAF1RAF1_P330_F−1730.0230.0220.49
cg154384973HLTFSMARCA3_P17_R460.1030.0810.20
cg246213547TESTES_P182_F−170.0770.0940.15
cg208790857TESTES_P182_F420.0610.0630.93
cg197438817TESTES_P182_F390.0920.0940.92
cg163793377TESTES_P182_F510.0840.0700.60
cg002540797TESTES_P182_F−230.0350.0490.16
cg031271748TUSC3TUSC3_E29_R−280.0790.0830.83
cg181458778TUSC3TUSC3_E29_R−300.0570.0610.88
cg030320988TUSC3TUSC3_E29_R1400.1120.0940.46
  • aInfinium 450K probes targeting CpG loci within 200 bp of the GoldenGate probes were assessed for racial differences in methylation in breast tumors from 42 AAs and 291 whites in TCGA; negative value indicates the 450K probe was 5′ of the GoldenGate probe.

  • bP values determined by the t test. There were no 450K probes for HBII-52 (alias SNORD115-1) within 200 bp of the GoldenGate probe.

  • cThis 450K probe interrogates a CpG site (cg12504148) that is 55 bp upstream of the CpG targeted by the DNAJC15_E26_R GoldenGate probe.