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. 2018 Jul 17;9:258. doi: 10.3389/fgene.2018.00258

Table 6.

Risk assessment and diagnostic value of 13 CPG sites of DAPK1 promoter for CC.

CPG sites Locationa CPG featuresb Studies Nc Sample size (CC/controls) Risk assessment of CPG sites for CC Diagnostic value of CPG sites in CC
Heterogeneity Effect size Cut-off β value Specificity (%) Sensitivity (%) AUC
I2(%) PQ–test Modeld SMD (95%CI) P
cg08719486 chr9: 87497186 N_shore 7 643/245 80 <0.001 R 2.44 (2.16, 2.72) 1.08 × 10−104 0.566 90 81 0.95
cg13823120 chr9: 87497210 N_shore 4 587/71 55 0.083 R 1.08 (0.43, 1.74) 0.001 0.429 85 60 0.77
cg13814950 chr9: 87497600 Island 7 643/245 9 0.357 F 0.86 (0.61, 1.10) 1.07 × 10−20 0.079 97 33 0.63
cg22571217 chr9: 87497604 Island 7 643/245 42 0.108 F 0.87 (0.63, 1.12) 7.37× 10−20 0.097 97 34 0.70
cg13932603 chr9: 87497600 Island 4 587/71 0 0.892 F 0.85 (0.49, 1.22) 3.40 × 10−11 0.062 74 71 0.74
cg20401521 chr9: 87497796 Island 4 587/71 0 0.769 F 1.17 (0.80, 1.54) 5.66 × 10−13 0.070 76 70 0.76
cg08797471 chr9: 87498205 Island 7 643/245 51 0.059 R 1.01 (0.57, 1.45) 1.19 × 10−45 0.162 75 78 0.80
cg19734228 chr9: 87498678 Island 7 643/245 38 0.142 F 1.13 (0.89, 1.38) 1.59 × 10−50 0.173 84 73 0.87
cg15746719 chr9: 87498898 Island 7 643/245 77 <0.001 R 1.67 (0.95, 2.40) 3.05 × 10−58 0.166 80 72 0.83
cg14014720 chr9: 87499083 S_shore 4 587/71 76 0.006 R 0.59 (−0.29, 1.47) 0.190 0.200 58 51 0.47
cg13527872 chr9: 87499122 S_shore 2 309/31 0 0.581 F −0.49 (−1.27, 0.28) 0.212 0.403 56 51 0.46
cg24754277 chr9: 87499241 S_shore 7 643/245 79 <0.001 R 0.76 (0.08, 1.44) 0.028 0.344 61 62 0.74
cg13752933 chr9: 87499840 S_shore 4 587/71 76 0.006 R 0.13 (−0.75, 1.00) 0.776 0.334 61 43 0.31

N, number; CC, cervical cancer; SMD, standardized mean differences; AUC, area under the curve.

a

Information for chromosome position is based on NCBI genome build 38.2.°

b

According to the TCGA data user's guide, Island means the start coordinates of the CPG island; N_shore means 0-2 kb upstream from the position of the CPG island; S_shore means 0-2 kb downstream from the position of the CPG island.

c

TCGA CESC, GSE68339, GSE99511, and GSE46306 used the Illumina 450 K BeadChip, which included methylation probes of all 13 CPG sites in DAPK1 promoter; another three datasets (GSE30760, GSE36637, and GSE41384) used 27 K BeadChip, which detected seven CPG sites, including cg08719486, cg13814950, cg22571217, cg08797471, cg19734228, cg15746719, and cg24754277.

d

When significant heterogeneity was found (I2 ≥ 50% or PQ−test ≤ 0.1), a random-effects model with the inverse variance method was used to pool the results; otherwise, a fixed-effects model was applied.

Bold values indicate significant results with P values < 10-7.