Diagnostic markers of urothelial cancer based on DNA methylation analysis

BMC Cancer

Table 3 ROC analysis of DNA methylation markers for UC

Gene	Cut-off value (%)	AUC	Sensitivity (%)	Specificity (%)	P value
Validation in tissue (N/CN vs. T)
Hypermethylation
SOX1	32.59	0.97	93.62	97.5	5.13E-14
TJP2	71.42	0.92	84.91	97.78	1.19E-12
MYOD	26.0	0.91	75.0	79.83	1.73E-12
HOXA9_1	55.59	0.86	76.6	97.83	9.00E-08
HOXA9_2	29.06	0.86	83.02	97.83	5.22E-10
Hypomethylation
VAMP8	12.5	0.96	94.34	97.83	2.22E-15
CASP8	23.18	0.96	94.34	95.65	4.88E-15
SPP1	26.14	0.95	86.79	100	1.49E-14
IFNG	64.7	0.93	82.98	95.65	2.16E-12
CAPG	16.21	0.93	83.02	95.65	1.08E-12
HLADPA1	14.31	0.88	84.62	86.96	1.06E-09
RIPK3	22.97	0.85	81.63	84.44	9.54E-07
Validation in tissue (N vs. CN)
Hypermethylation
SOX1	16.51	0.86	68.18	100	9.04E-05
MYOD	12.71	0.85	76.0	85.71	5.19E-05
HOXA9_1	22.95	0.80	76.0	80.95	0.00043
GALR1	7.24	0.85	76.0	85.71	4.26E-05
IPF1	33.83	0.74	64.0	76.19	0.0089
TAL1	29.47	0.83	76.0	85.71	0.00011
EYA4	6.38	0.80	83.33	73.68	0.0078
CDH13	7.13	0.93	88.0	85.71	5.24E-07
CYP1B	13.61	0.75	60.0	80.95	0.0040
NPY	10.31	0.82	88.0	71.43	0.00018
Hypometylation
CASP8	46.38	0.73	60.0	85.71	0.0084
IFNG	84.93	0.78	56.0	95.24	0.001
HLADPA1	24.27	0.83	72.0	85.71	0.00011
Validation in urine sediment (NU vs. TU)
Hypermethylation
SOX1	15.62	0.74	41.54	100	0.0041
TJP2	7.933	0.79	92.54	56.25	0.0003
MYOD	9.897	0.93	86.79	87.50	3.10E-05
HOXA9_1	7.038	0.92	86.23	88.89	4.25E-05
HOXA9_2	3.20	0.81	88.57	61.54	0.0004
Hypomethylation					10.78
VAMP8	10.78	0.72	97.06	40.0	0.023
CASP8	7.863	0.82	73.61	76.92	0.0005
SPP1	21.23	0.79	85.94	75.0	0.0015
IFNG	86.08	0.76	55.07	92.31	0.0037
CAPG	8.08	0.67	83.82	56.25	0.04
HLADPA1	6.46	0.82	77.19	90.0	0.0009
RIPK3	9.37	0.75	82.35	70.0	0.011

Selected loci that were identified as either hyper- or hypo-methylated were analyzed for their degree of DNA methylation and association with UC. The loci are named by the genes in which they occur; if there are 2 loci in the same gene, the suffixes 1 and 2 are added.

ISSN: 1471-2407