Table 2. . Hazard ratios and 95% confidence intervals for the top associations between methylation in CpG loci and overall survival, disease-specific survival and progression-free interval.
| CpG site | Chr | Position | UCSC gene name | UCSC gene group | Chromatin state | β-value, mean (SD) | Expression | Overall survival |
Disease-specific survival |
Progression-free interval |
|
|---|---|---|---|---|---|---|---|---|---|---|---|
| Spearman's ρ | p-value | HR (95% CI)† | HR (95% CI)† | HR (95% CI)† | |||||||
| IL10 | |||||||||||
| cg14789529 | chr1 | 206941464 | IL10 | 3′UTR | Weak transcription | 0.75 (0.09) | -0.229 | <0.001 | 0.70 (0.56, 0.89) | 0.68 (0.52, 0.88) | 0.80 (0.64, 1.00) |
| TGFβ2 | |||||||||||
| cg16361301 | chr1 | 218519549 | TGFβ2 | 1st Exon; 5′UTR | Active TSS | 0.05 (0.02) | 0.009 | 0.900 | 1.14 (0.93, 1.39) | 1.15 (0.91, 1.45) | 1.23 (1.01, 1.51) |
| cg20698667 | chr1 | 218523325 | TGFβ2 | Body | Weak transcription | 0.65 (0.14) | -0.173 | 0.020 | 1.34 (1.04, 1.74) | 1.36 (1.03, 1.81) | 1.17 (0.93, 1.46) |
| cg07810039 | chr1 | 218524558 | TGFβ2 | Body | Weak transcription | 0.46 (0.21) | -0.436 | <0.001 | 0.81 (0.64, 1.01) | 0.74 (0.57, 0.97) | 0.79 (0.64, 0.99) |
| cg16967578 | chr1 | 218575437 | TGFβ2 | Body | Weak transcription | 0.80 (0.11) | 0.099 | 0.190 | 1.45 (1.03, 2.02) | 1.52 (1.05, 2.20) | 1.50 (1.08, 2.09) |
| IL8 | |||||||||||
| cg04392234 | chr4 | 74608458 | IL8 | 3′UTR | Quiescent/low | 0.82 (0.09) | -0.048 | 0.520 | 0.86 (0.61, 1.22) | 0.70 (0.48, 1.02) | 0.51 (0.36, 0.72) |
| TNF | |||||||||||
| cg17741993 | chr6 | 31544694 | TNF | Body | Quiescent/low | 0.78 (0.13) | -0.396 | <0.001 | 1.26 (0.98, 1.62) | 1.35 (1.02, 1.78) | 1.12 (0.88, 1.42) |
| cg20477259 | chr6 | 31544960 | TNF | Body | Quiescent/low | 0.55 (0.10) | -0.227 | <0.001 | 1.35 (1.05, 1.74) | 1.39 (1.06, 1.83) | 1.11 (0.86, 1.44) |
| cg09637172 | chr6 | 31545252 | TNF | Body | Weak transcription | 0.84 (0.13) | -0.389 | <0.001 | 1.38 (1.01, 1.89) | 1.48 (1.05, 2.08) | 1.08 (0.81, 1.44) |
| cg05952498 | chr6 | 31545257 | TNF | Body | Weak transcription | 0.74 (0.13) | -0.363 | <0.001 | 1.34 (0.98, 1.85) | 1.55 (1.10, 2.20) | 1.11 (0.80, 1.55) |
| cg02137984 | chr6 | 31545898 | TNF | 3′UTR | Weak transcription | 0.87 (0.07) | -0.463 | <0.001 | 1.33 (1.02, 1.74) | 1.47 (1.09, 1.99) | 1.10 (0.88, 1.37) |
| IL6 | |||||||||||
| cg26061582 | chr7 | 22766209 | IL6 | TSS1500 | Enhancers | 0.07 (0.07) | -0.037 | 0.620 | 0.66 (0.44, 0.98) | 0.72 (0.46, 1.12) | 0.87 (0.63, 1.19) |
| TGFβ3 | |||||||||||
| cg06958766 | chr14 | 76446087 | TGFβ3 | Body | Active TSS | 0.66 (0.16) | -0.178 | 0.020 | 1.16 (0.91, 1.49) | 1.17 (0.88, 1.53) | 1.32 (1.05, 1.67) |
| cg24696715 | chr14 | 76446681 | TGFβ3 | Body | Flanking Active TSS | 0.57 (0.08) | -0.479 | <0.001 | 0.80 (0.63, 1.01) | 0.76 (0.58, 0.99) | 0.89 (0.71, 1.11) |
| cg16292972 | chr14 | 76448509 | TGFβ3 | TSS1500 | Active TSS | 0.04 (0.01) | 0.071 | 0.350 | 1.26 (1.01, 1.57) | 1.22 (0.95, 1.57) | 1.06 (0.86, 1.31) |
| TGFβ1 | |||||||||||
| cg09926389 | chr19 | 41837123 | TGFβ1 | Body | Weak transcription | 0.73 (0.19) | 0.378 | <0.001 | 1.34 (1.03, 1.73) | 1.42 (1.05, 1.92) | 1.29 (0.99, 1.66) |
| cg03630756 | chr19 | 41839506 | TGFβ1 | Body | Weak transcription | 0.92 (0.02) | 0.066 | 0.380 | 0.77 (0.53, 1.13) | 0.64 (0.42, 0.96) | 0.95 (0.67, 1.36) |
| cg03313751 | chr19 | 41857626 | TGFβ1 | Body | Flanking active TSS | 0.03 (0.01) | -0.316 | <0.001 | 1.21 (0.99, 1.47) | 1.22 (0.98, 1.53) | 1.22 (1.02, 1.47) |
| cg04547554 | chr19 | 41860013 | TGFβ1 | TSS200 | Flanking Active TSS | 0.02 (0.01) | -0.175 | 0.020 | 1.19 (1.00, 1.43) | 1.25 (1.03, 1.52) | 1.02 (0.79, 1.32) |
| cg23275502 | chr19 | 41860019 | TGFβ1 | TSS200 | Flanking active TSS | 0.02 (0.02) | -0.161 | 0.030 | 1.18 (1.01, 1.37) | 1.23 (1.04, 1.45) | 0.85 (0.40, 1.80) |
| cg24767336 | chr19 | 41860095 | TGFβ1 | TSS1500 | Flanking active TSS | 0.03 (0.02) | -0.160 | 0.030 | 1.30 (1.13, 1.50) | 1.32 (1.12, 1.57) | 1.04 (0.82, 1.33) |
†
Fully adjusted models adjusted for age, sex, race, stage and six surrogate variables.
Models were run using complete case analysis. Maximum sample sizes were 181 for overall survival, 174 for disease-specific survival and 181 for progression-free interval.
p-values and q-values for Cox proportional hazards models can be found in Supplementary Table 1.
TSS: Transcription start site.