Table 1.

Twenty-six CpG loci identified in sample set #1 exhibiting significant promoter methylation differences and β-value differences ≥0.2 between primary melanomas and nevi after adjustment for age, sex, and Bonferroni correction for multiple comparisons

			Sample set 1					Sample set 2
Gene symbol	CpG probe	Gene description	Nevus mean β	Melanoma mean β	P-value1	Mean Δβ	AUC	AUC
Hypermethylated in melanomas compared with nevi (n = 7)
COL1A2	E299_F	Collagen, type I, alpha 2	0.065	0.623	4.07 × 10−5	−0.558	0.9007	0.6248
FRZB	P406_F	Frizzled-related protein	0.039	0.374	1.45 × 10−2	−0.334	0.8986	0.7613***
GSTM2	P453_R	Glutathione S-transferase M2	0.145	0.590	6.31 × 10−3	−0.445	0.9186	0.5731
KCNK4	E3_F	Potassium channel, subfamily K, member 4	0.089	0.479	2.62 × 10−3	−0.390	0.9057	0.7600
NPR2	P1093_F	Natriuretic peptide receptor B/guanylate cyclase B	0.564	0.833	1.78 × 10−2	−0.269	0.8434	0.6581
TRIP6	P1090_F	Thyroid hormone receptor interactor 6	0.099	0.667	6.30 × 10−5	−0.568	0.8518	0.7186
TRIP6	P1274_R	Thyroid hormone receptor interactor 6	0.187	0.705	2.71 × 10−3	−0.518	0.8704	0.5945
Hypomethylated in melanomas compared with nevi (n = 19)
CARD15/NOD2	P302_R	Caspase recruitment domain family, member 15	0.560	0.114	3.09 × 10−2	0.446	0.8754	0.7874**
CD2	P68_F	CD2 molecule	0.961	0.735	1.26 × 10−7	0.227	0.9983	0.8414*
EMR3	E61_F	EGF-like module-containing mucin-like hormone receptor-like 3	0.921	0.485	1.35 × 10−3	0.436	0.9242	0.9503*
EMR3	P39_R	EGF-like module-containing mucin-like hormone receptor-like 3	0.920	0.633	2.00 × 10−3	0.286	0.9259	0.8391*
EV12A	P94_R	Ecotropic viral integration site 2A	0.783	0.265	1.35 × 10−3	0.518	0.9592	0.9669*
HLA-DPA1	P28_R	Major histocompatibility complex, class II, DP alpha 1	0.902	0.565	3.32 × 10−2	0.337	0.9191	0.8400*
IFNG	P459_R	Interferon gamma	0.915	0.634	7.91 × 10−9	0.281	0.9630	0.9670*
IL2	P607_R	Interleukin 2	0.887	0.590	8.97 × 10−3	0.297	0.9489	0.8801*
ITK	P114_F	IL2-inducible T-cell kinase	0.924	0.632	2.68 × 10−6	0.292	0.9663	0.9076*
KLK10	P268_R	Kallikrein-related peptidase 10	0.673	0.257	4.38 × 10−2	0.417	0.9040	0.6997
LAT	E46_F	Linker for activation of T cells	0.895	0.540	1.75 × 10−2	0.355	0.9646	0.8328*
MPO	P883_R	Myeloperoxidase	0.759	0.165	2.39 × 10−6	0.593	0.9983	0.8908*
PSCA	E359_F	Prostate stem cell antigen	0.859	0.658	5.17 × 10−3	0.201	0.8788	0.6028
PTHLH	E251_R	Parathyroid hormone-like hormone	0.923	0.602	5.80 × 10−6	0.322	0.9933	0.8497*
PTHR1	P258_F	Parathyroid hormone receptor 1	0.849	0.593	4.56 × 10−3	0.256	0.8889	0.5848
RUNX3	P393_R	Runt-related transcription factor 3	0.967	0.735	3.26 × 10−8	0.232	1.0000	0.9200*
RUNX3	E27_R	Runt-related transcription factor 3	0.960	0.665	6.53 × 10−8	0.296	0.9983	0.9393*
RUNX3	P247_F	Runt-related transcription factor 3	0.964	0.627	1.06 × 10−8	0.337	1.0000	0.9324*
TNFSF8	E258_R	Tumor necrosis factor superfamily, member 8	0.952	0.599	1.64 × 10−7	0.353	0.9949	0.9462*

¹P-value, nevus mean β, and melanoma mean β were each adjusted for age, sex, and multiple comparisons using Bonferroni correction.

AUC; area under the ROC curve.

P-value significant for difference between melanomas and nevi in sample set #2 at the 0.05* or 0.0505** level after adjustment for age, sex, and multiple comparisons using Bonferroni correction. ***FRZB_P406_F (AUC of 0.7613) was not significantly differentially methylated in sample set #2; however, a different CpG site within the FRZB gene (FRZB_E186_R) was with AUC of 0.8648.