Targeted bisulfite sequencing identified a panel of DNA methylation-based biomarkers for esophageal squamous cell carcinoma (ESCC)

Table 2 The methylation status of the five CpG sites in the TCGA dataset and the validation dataset

	CpG site	Gene	Position	Relation to CpG_Island	McaM^b	McoM^b	P value^c	log₁₀(OR)^d	95% CI^d	Sens	Spec	AUC
TCGA	cg15830431	STK3	chr8:99952591	Island	0.28	0.09	2.20E−04	4.11	1.91–7.43	0.65	0.94	0.82
	cg19396867	NA^a	chr19:40314862	N_Shore	0.45	0.20	3.60E−04	1.85	0.78–3.21	0.85	0.75	0.79
	cg20655070	NA^a	chr19:40315011	Island	0.44	0.19	1.71E−03	1.61	0.67–2.72	0.64	0.88	0.75
	cg26671652	ZNF418	chr19:58446312	N_Shore	0.35	0.16	5.77E−04	1.95	0.67–3.61	0.86	0.75	0.78
	cg27062795	ZNF542	chr19:56879613	Island	0.43	0.17	3.60E−04	2.93	1.65–4.44	0.86	0.81	0.80
Validation	cg15830431	STK3	chr8:99952591	Island	0.20	0.07	1.25E−06	3.04	1.82–4.53	0.66	0.77	0.71
	cg19396867	NA	chr19:40314862	N_Shore	0.37	0.12	2.71E−11	2.83	1.93–3.91	0.65	0.88	0.80
	cg20655070	NA	chr19:40315011	Island	0.31	0.09	8.04E−10	3.01	2.02–4.22	0.62	0.89	0.77
	cg26671652	ZNF418	chr19:58446312	N_Shore	0.32	0.11	4.82E−11	3.20	2.18–4.39	0.58	0.93	0.79
	cg27062795	ZNF542	chr19:56879613	Island	0.43	0.12	1.23E−12	2.55	1.77–3.50	0.72	0.82	0.83

The sensitivity and specificity, as well as AUC, were both with a logistic regression prediction model without adjustment for gender, age, and smoking status and alcohol status
Sens sensitivity, Spec specificity, AUC area under the curve
^aNA indicated that the CpG site is located outside of the coding region of the gene
^bMcaM represents the mean methylation percentage of the cases, and the McoM represents the mean methylation percentage of the controls
^c P value is calculated through the Wilcoxon rank-sum test followed by FDR (false discovery rate) adjustment for multiple correction
^dOR and 95% CI were determined by logistic regression

ISSN: 1868-7083