Table 3. Table of top cfDNA DMRs identified based on comparing pre- and post-treatment cfDNA methylation profiles by considering different patient subgroups.
| Patient group/subgroup | Subset rationale | Top cfDNA DMRs (hg19)† |
|---|---|---|
| Paired samples from P1, P4, P7, and P8 | Patterns most consistent with TCGA results | chr7:37956001-37957000 (SFRP4) chr8:67873001-67874000 (TCF24) chr2:45171001-45172000 (SIX3*) chr11:32458001-32459000 (WT1-AS) chr8:53478001-53479000 (ALKAL1) chr8:57358001-57359000 (PENK) chr13:93879001-93880000 (GPC6) chr8:55370001-55371000 (SOX17) chr4:183062001-183063000 (TENM3-AS1*) chr1:119535001-119536000 (TBX15*) chr19:58095001-58096000 (ZIK1) |
| Paired samples from P1, P2, P3, and P7 | Patients with T4 tumors (male patients) | chr7:37956001-37957000 (SFRP4) chr1:47696001-47697000 (TAL1) chr5:1594001-1595000(SDHAP3) chr7:87257001-87258000 (ABCB1/RUNDC3B) chr8:57358001-57359000(PENK) |
| Paired samples from P3, P5, P6, and P7 | Tongue site only | chr11:43602001-43603000 (MIR129-2) |
| P4, P6, and P8 | Female patients only | No region significant at 10−7 level |
| Paired samples from P1, P2, P3, P4 and P7 | All T4 patients+ P4 (signature patient) | chr7:37956001-37957000 (SFRP4) chr8:57358001-57359000 (PENK) chr8:55370001-55371000 (SOX17) chr3:129693001-129694000 (TRH) chr14:48143001-48144000 (MDGA2*) chr14:48145001-48146000 (MDGA2) |
| Paired samples from P1, P2, P3, P4, P6, P7, and P8 | All patients except P5 (potential outlier) | chr8:57358001-57359000 (PENK) chr7:37956001-37957000 (SFRP4) chr8:55370001-55371000 (SOX17) |
†
Unless otherwise specific, DMRs are significant at 0.1 level for adjusted p-value or at 10−7 level for unadjusted p-value. DMRs not in the promoter region of the gene are indicated by “*”.