Comparison of quantification algorithms for circulating cell-free DNA methylation biomarkers in blood plasma from cancer patients

Table 1 Diagnostic and prognostic performance of SHOX2 and SEPT9 hypermethylation

Cohort	Biomarker	Quantification method	Sens. (%)	Spec. (%)	AUC	Hazard ratio	P value	95% CI
Training
	SEPT9	Relative	63	90	0.80	1.23	< 0.001	1.11–1.35
		Absolute	61	90	0.80	1.27	< 0.001	1.14–1.42
		Quasi-digital PCR	62	92	0.79	1.90	< 0.001	1.34–2.69
	SHOX2	Relative	57	90	0.81	1.14	0.009	1.03–1.26
		Absolute	55	90	0.80	1.16	0.013	1.03–1.31
		Quasi-digital PCR	53	87	0.78	1.85	0.008	1.18–2.91
	Mean_SEPT9/SHOX2	Relative	64	90	0.84	1.19	0.001	1.07–1.32
		Absolute	64	90	0.83	1.22	0.001	1.08–1.37
		Quasi-digital PCR	65	91	0.81	1.89	0.001	1.28–2.79
Testing
	SEPT9	Relative	56	88	0.74	1.22	0.002	1.07–1.38
		Absolute	54	89	0.74	1.35	0.001	1.45–1.59
		Quasi-digital PCR	55	90	0.75	1.67	0.010	1.13–2.45
	SHOX2	Relative	48	93	0.79	1.15	0.045	1.00–1.31
		Absolute	43	94	0.78	1.24	0.007	1.06–1.44
		Quasi-digital PCR	43	95	0.77	1.71	0.032	1.05–2.80
	Mean_SEPT9/SHOX2	Relative	58	94	0.80	1.12	0.006	1.06–1.39
		Absolute	49	90	0.80	1.30	0.001	1.11–1.53
		Quasi-digital PCR	58	88	0.80	1.77	0.009	1.15–2.72

Clinical performance was evaluated in HNSCC patients included in a training and a testing cohort. Methylation levels were calculated using three different algorithms (relative, absolute quantification, and quasi-digital PCR). Sensitivities (sens.), specificities (spec.), Area Under the Curve (AUC) of the Receiver Operating Characteristic, and Cox Proportional Hazards with univariate analysis of SEPT9, SHOX2, and mean_SEPT9/SHOX2, corresponding p values, and 95% confidence intervals are reported

ISSN: 1868-7083