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, bpb
Location in promoter CGIc
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
Yes
0.00
0.68
0.02
ISL1_P554_F
5
50714472
cg16203270
Yes
0.42
0.87
0.04
LY6G6E_P45_R
6
31789613
cg26399860
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
Yes
0.54
0.03
0.00
MST1R_P87_R
3
49916161
cg01709977
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
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
No
0.36
0.63
0.01
THBS2_P605_Rd
6
169396667
cg24654845
No
0.21
0.62
0.08
Probe annotation according to the Illumina GoldenGate Cancer Panel I methylation assay. Distance in bp of CpG locus to transcription start site. CpG Island. Results reported by Houshdaran et al. [36] at FDR < 5%.