Differentially Methylated Loci Distinguish Ovarian Carcinoma Histological Types: Evaluation of a DNA Methylation Assay in FFPE Tissue

Table 2

Median β-values across ovarian carcinoma types for loci with FDR < 0.1% using 400 ng bsDNA.

Target CpG (Gene_Probe)^a	Chr	Coordinate, bp	CpG locus ID	Distance to TSS, bp^b	Location in promoter CGI^c	Median β-value			Pairwise comparison
						Serous	Clear cell	Endometrioid
ERG_E28_F	21	38955460	cg12571150	28	Yes	0.00	0.72	0.10	Serous versus Clear cell
ERG_E28_F	21	38955460	cg12571150	28	Yes	0.00	0.72	0.10	Clear cell versus Endometrioid
ISL1_E87_R	5	50715113	cg13836786	132	Yes	0.10	0.50	0.03	Clear cell versus Endometrioid
ISL1_P379_F	5	50714647	cg14024101	−379	Yes	0.00	0.68	0.02
ISL1_P554_F	5	50714472	cg16203270	−554	Yes	0.42	0.87	0.04
LY6G6E_P45_R	6	31789613	cg26399860	−1499	No	0.20	0.80	0.01	Clear cell versus Endometrioid
MST1R_E42_R	3	49916032	cg03714052	42	Yes	0.81	0.69	0.11	Clear cell versus Endometrioid
MST1R_P392_F	3	49916466	cg03610760	−392	Yes	0.54	0.03	0.00
MST1R_P87_R	3	49916161	cg01709977	−87	Yes	0.59	0.33	0.07
NRG1_E74_F	8	32525369	cg25833018	74	Yes	0.30	0.01	0.00	Clear cell versus Endometrioid
NRG1_P558_R	8	32524737	cg12863621	−558	Yes	0.21	0.72	0.01
THBS2_E129_F	6	169395933	cg05068443	129	Yes	0.13	0.00	0.01	Clear cell versus Endometrioid
THBS2_P605_R	6	169396667	cg24654845	−605	No	0.36	0.63	0.01
THBS2_P605_R^d	6	169396667	cg24654845	−605	No	0.21	0.62	0.08

aProbe annotation according to the Illumina GoldenGate Cancer Panel I methylation assay.
bDistance in bp of CpG locus to transcription start site.
cCpG Island.
dResults reported by Houshdaran et al. [36] at FDR < 5%.