Table 2.

Genomic regions of agglomerative epigenetic aberrations in breast cancer

ChromosomeFrom (bp)To (bp)Size (kbp)No of DMRsFrequency * (% of patients)Genes within region
Hypermethylated in tumors
    chr11656750416838375271833BC006312, AK123337
    chr21767715431768807411091344HOXD13, HOXD11, HOXD10, HOXD9, AK092134, HOXD8, HOXD4, HOXD3
    chr51401459471402877451421150AK091409, PCDHA1, PCDHA10, PCDHA11, PCDHA12, PCDHA13, PCDHA2, PCDHA3, PCDHA4, PCDHA5, PCDHA6, PCDHA7, PCDHA8, PCDHA9, PCDHAC1
    chr51404555381408389403833267BC031837, BC051788, PCDHB10, PCDHB11, PCDHB12, PCDHB13, PCDHB14, PCDHB15, PCDHB16, PCDHB17, PCDHB18, PCDHB2, PCDHB3, PCDHB4, PCDHB5, PCDHB6, PCDHB7, PCDHB8, PCDHGA1, PCDHGA10, PCDHGA11, PCDHGA12, PCDHGA2, PCDHGA3, PCDHGA4, PCDHGA5, PCDHGA6, PCDHGA7, PCDHGA8, PCDHGA9, PCDHGB1, PCDHGB2, PCDHGB3, PCDHGB4, PCDHGB5, PCDHGB6, PCDHGB7, PCDHGC3, SLC25A2, TAF7
    chr6262908242638175491828HIST1H2BE, HIST1H4D, HIST1H3D, HIST1H2AD, BC056264, HIST1H2BF, HIST1H4E, BC082232, HIST1H2BG, HIST1H2AE, HIST1H3E, HIST1H1D, HIST1H4F, HIST1H4G, HIST1H3F, HIST1H2BH, HIST1H3G, HIST1H2BI
    chr63327311933532803260922RXRB, X66424, SLC39A7, HSD17B8, RING1, VPS52, BC040114, AK093057, AK001725, RPS18, AY536376, B3GALT4, C6orf11, HKE2, RGL2, AB012295, BC064966, BC080574, TAPBP, ZNF297, DAXX, AF090423, KIFC1, PHF1, C6orf82, SYNGAP1, AB067525, ZBTB9
    chr726909767270558751461344HOXA3, AK056230, HOXA4, HOXA5, HOXA6, HOXA7, HOXA9, HOXA10, BC007600, HOXA11, HOXA13
Hypomethylated in tumors
    chr12446109732451718045612339OR2M2, OR2M3, OR2M4, OR2T33, OR2T12, OR2M7, OR5BF1, OR2T4, OR2T1, OR2T2, OR2T3, OR2T5, OR2G6, OR2T29, OR2T34, OR2T10, OR2T11, OR2T35
    chr490193579047147281289DUB3, AY533200
    chr517551068176420399196no genes
    chr8682602369345571091222DEFA1, DEFA3, DEFA5
    chr8706120173159812551856DEFB4, DEFB103A, SPAG11, DEFB104A
    chr877291747935902207839DEFB4, DEFB103A, SPAG11, DEFB104A
    chr1959862651600760002132639KIR2DL1, KIR2DL3, KIR2DL4, KIR2DS2, KIR2DS4, KIR3DL1, KIR3DL2, KIR3DL3, KIR3DP1, L76664, L76668, LILRB4, U33328, X93596, X99481, AF002256, AF276292, AF283988, AY102623, AY366253, AY601812, BC028206, BC069344, CR609786
    chrX48930476491639282331828GAGE1, GAGE2, GAGE4, GAGE5, GAGE6, BC036094, BC081536
  • NOTE: DMRs were grouped together when the distance between them was smaller than 100 kb. Regions with clusters of ≥8 consecutive DMRs are shown.

  • * Frequency represents the percentage of tumors in which aberrant methylation occurs in at least 75% of all DMRs within the analyzed region.