DNA Methylation Levels of Melanoma Risk Genes Are Associated with Clinical Characteristics of Melanoma Patients

Table 2

Methylation levels of melanoma susceptibility genes in primary melanomas and melanocyte primary cultures from healthy donors.

Gene name	Chromosome	UCSC accession (transcripts)	Genic region	CpG loci number	Melanomas (SD)	Melanocytes (SD)	value
BAP1	3	NM_004656	Body	5	0.52 (0.44)	0.44 (0.46)	1.00
		NM_004656	Promoter	10	0.04 (0.01)	0.05 (0.02)	0.16
CDK4	12	NM_000075	Body	2	0.18 (0.09)	0.06 (0.02)	—
		NM_000075	Promoter	13	0.22 (0.30)	0.22 (0.30)	0.54
CDKN2A	9	NM_058195	Promoter	4	0.12 (0.03)	0.08 (0.05)	0.20
KIT	4	NM_000222, NM_001093772	Body	9	0.50 (0.30)	0.17 (0.28)	0.01
			Promoter	5	0.32 (0.24)	0.08 (0.08)	0.03
MC1R	16	NM_002386	Promoter	9	0.27 (0.32)	0.07 (0.05)	0.67
MGMT	10	NM_002412	Promoter	14	0.42 (0.35)	0.44 (0.42)	0.99
		NM_002412	Body	99	0.74 (0.15)	0.83 (0.20)	<1
MITF	3	NM_000248	Promoter	3	0.53 (0.09)	0.06 (0.05)	0.1
		NM_000248	Body	5	0.79 (0.20)	0.57 (0.45)	0.42
		NM_006722	Promoter	4	0.79 (0.10)	0.80 (0.16)	0.89
		NM_006722	Body	20	0.78 (0.17)	0.64 (0.38)	0.78
		NM_198158	Promoter	3	0.53 (0.09)	0.06 (0.05)	0.10
		NM_198158	Body	5	0.79 (0.20)	0.57 (0.45)	0.42
		NM_198159	Promoter	5	0.04 ()	0.04 ()	0.55
		NM_198159	Body	29	0.67 (0.29)	0.56 (0.39)	0.77
		NM_198177	Promoter	4	0.77 (0.16)	0.59 (0.29)	0.20
		NM_198177	Body	14	0.77 (0.19)	0.61 (0.42)	0.84
		NM_198178	Promoter	2	0.94 (0.04)	0.97 (0.01)	—
		NM_198178	Body	10	0.73 (0.20)	0.48 (0.43)	0.28
PALB2	16	NM_024675	Body	5	0.22 (0.40)	0.22 (0.39)	0.84
		NM_024675	Promoter	12	0.07 (0.08)	0.08 (0.09)	0.37
POT1	7	NM_001042594	Body	1	0.95 (0.04)	0.94 (0.01)	—
		NM_001042594	Promoter	10	0.12 (0.23)	0.14 (0.26)	0.31
		NM_015450	Body	1	0.95 (0.04)	0.94 (0.01)	—
		NM_015450	Promoter	10	0.12 (0.23)	0.14 (0.26)	0.31
		NR_003102, NR_003103, NR_003104	Body	3	0.33 (0.53)	0.33 (0.52)	0.70
		NR_003102, NR_003103, NR_003104	Promoter	7	0.16 (0.27)	0.19 (0.30)	0.71
TERT	5	NM_198255, NM_198253	Body	61	0.67 (0.13)	0.71 (0.19)	0.03
		NM_198253, NM_198255	Promoter	6	0.52 (0.24)	0.38 (0.24)	0.49
TNFRSF10C	8	NM_003841	Promoter	13	0.54 (0.17)	0.47 (0.32)	0.64
		NM_003841	Body	3	0.47 (0.13)	0.34 (0.38)	0.70
TNF	6	NM_000594	Body	5	0.76 (0.06)	0.89 (0.07)	0.01
		NM_000594	Promoter	13	0.54 (0.17)	0.47 (0.32)	0.64

SD: standard deviation; promoter: probes mapped at TSS1500, TSS200, 5′UTR, or 1st exon; values highlighted in bold are statistically significant (, Mann-Whitney test).