Table 1.

Genetic and epigenetic features of the biomarkers of panel EpiWNT-SHH and panel EpiG3-G4

EpiWNT-SHHCpG 1CpG 2CpG 3CpG 4CpG 5CpG 6
TargetID-Illumina arraycg25542041cg02227036cg10333416cg12925355cg18849583cg01268345
Gene nameLHX6CHTF18USP40AKAP6KIAA1549
Gene-related RegionIntronIntergenicIntronIntron5prime_UTRExon
Chromosome916162147
Location (hg19)1249820875042532984447423438647132836157138603645
CpG IslandIslandOutside CGIShoreShoreOut_CGIOutside CGI
Regulatory function (E81)Enh BivEnh BivQuiescentEnhancerEnhancerEnhancer
TFBS (161 ENCODE)EZH2; RBBP5; SUZ12POLR2ARAD21
Median of DNA methylation levels (min–max)a
WNTMethylated 0.88Unmethylated 0.12Unmethylated 0.13Methylated 0.96Unmethylated 0.17Methylated 0.87
(0.57–0.94)(0.06–0.19)(0.06–0.2)(0.13–0.05)(0.05–0.12)(0.12–0.05)
SHHUnmethylated 0.09Methylated 0.91Methylated 0.9Unmethylated 0.11Unmethylated 0.16Methylated 0.88
(0.05–0.13)(0.81–0.95)(0.8–0.97)(0.06–0.17)(0.11–0.25)(0.64–0.94)
Group 3Unmethylated 0.08Methylated 0.92Unmethylated 0.12Methylated 0.97Methylated 0.88Unmethylated 0.10
(0.05–0.12)(0.8–0.98)(0.06–0.57)(0.93–0.99)(0.69–0.95)(0.03–0.33)
Group 4Unmethylated 0.09Methylated 0.92Unmethylated 0.16Methylated 0.96Methylated 0.90Unmethylated 0.07
(0.05–0.26)(0.9–0.95)(0.07–0.46)(0.94–0.98)(0.72–0.95)(0.04–0.17)
EpiG3-G4CpG 1CpG 2CpG 3CpG 4CpG 5
TargetID-Illumina arraycg13548946cg05679609cg09929238cg08129331cg12565585
Gene nameVPS37BRPTORRPTORRIMS2
Gene-related region3prime_UTRIntergenicIntron_1Intron_1Intron
Chromosome121217178
Location (hg19)123350077306719267856091678560478105235943
CpG IslandShoreOut_CGIOut_CGIOut_CGIIsland
Regulatory function (E81)Weak TranscriptionQuiescentQuiescentQuiescentEnhancer
TFBS (161 ENCODE)POLR2AE2F6; SPI1POLR2APOLR2ACTCF
Median of DNA methylation levels (min–max)a
Group 3Methylated 0.85Methylated 0.89Methylated 0.87Methylated 0.73Methylated 0.81
(0.65–0.91)(0.77–0.95)(0.62–0.96)(0.41–0.88)(0.24–0.95)
Group 4Unmethylated 0.24Unmethylated 0.20Unmethylated 0.16Unmethylated 0.13Unmethylated 0.06
(0.14–0.36)(0.06–0.56)(0.06–0.71)(0.05–0.44)(0.04–0.1)
  • Abbreviations: Enh Biv, enhancer bivalent; SHH, sonic hedgehog; TFBS, transcription factor binding sites (161 ENCODE); WNT, wingless.

  • aDNA methylation levels range from 0 for unmethylated to 1 for completely methylated.