Supplemental Table 1. Primers and probes used for MethyLight assay SOCS3


(%) 3, 4 (n=58) 

Table 2 .

 2 Mean and standard deviations of threshold cycle (Ct) values of five-times repeated MethyLight assays for eight genes in five pairs of fresh-frozen (FF) and formalin-fixed and paraffin embedded (FFPE) tissue samples. Supplemental Table3. Methylation frequency of each CpG island locus and its clinicopathological correlatons in 99 HCCs 


	DLEC1	3p22-	AP006309	19959-	Exon1	TCGTTGCGTATTT	CGTAACGCTCATT	6FAM-
		p21.3		20088		AAGATATTTCGTA	CTCGCTACC	TAATCAAACTTACGCT
						TT		CACTTCGTCGCCG-
								TAMRA
	GATA3 10p15	AL390294	51880-	Promoter TGTATCGGGACG	ACGCGCGCTCTAA	6FAM-
				51959		GAATCGTT	CCCTT	AAATATAACCGCGAC
								TCCTACCAATTCATTC
								G-TAMRA
	GRIN2B 12p12	AC007916	111645-	Promoter GTCGGATTTACGC	CTACCGCCGCGCT	6FAM-
				111727		GTCGAGT	AAAATAC	ACGCACGAAACTTCA
								CCTACAACGTATCG-
								TAMRA
	GSTP1	11q13	M24485	1146 -	Promoter/E	GTCGGCGTCGTGA	AAACTACGACGAC	6FAM-
				1245	xon1	TTTAGTATTG	GAAACTCCAA	AAACCTCGCGACCTC
								CGAACCTTATAAAA-
								TAMRA
	HOXA1 7p15	AC004079	78138-	Promoter GTTGTTGCGGCGA	CGCGCAAAACGCA	6FAM-
				78220		TTGTAAA	ACTT	TACTCTTCTTCGCTCC
								AACACTCCAAATCG-
								TAMRA
	IGF2	11p15.5 AC132217	108633-	Promoter/E	GAGCGGTTTCGGT	CCAACTCGATTTA	6FAM-
				108720	xon1	GTCGTTA	AACCGACG	CCCTCTACCGTCGCGA
								ACCCGA-TAMRA
	ITGA4	2q31-q32 AC020595	146569-	Exon1	TGCGGAGGCGTA	CAACCGAAATTCC	6FAM-
				146639		GGGTC	CCAACG	CCTACAACCGCGCGT
								AAACAAAAACG-
								TAMRA
	KL	13q12	AB009667	2062-	Promoter/E	AGTTTGGTTTTCG	CGCCCGACTCCGC	6FAM-
				2189	xon1	CGTAGTATGTTC	AC	CGAACGACGCGACGA
								AACGCT-BHQ-1
	MT1G	16q13	AC026461	19549-	Promoter CGTTTAAGGGATT	CCGCTAAATCCGC	6FAM-
				19625		TTGTATTTGGTTT	ACCG	CGCGATCCCGACCTA
						AT		AACTATACGCA-
								TAMRA
	NEUROG	5q23-q31 AC005738	75342-	Promoter CGTGTAGCGTTCG	CGATAATTACGAA	6FAM-
	1			75429		GGTATTTGTA	CACACTCCGAAT	CGATAACGACCTCCC
								GCGAACATAAA-
								TAMRA
	p16	9p21	AF527803	20012-	Exon1	TGGAGTTTTCGGT	AACAACGCCCGCA	6FAM-
				20081		TGATTGGTT	CCTCCT	ACCCGACCCCGAACC
								GCG-TAMRA
	PTGS2	1q25.2-	AF044206	6779 -	Promoter CGGAAGCGTTCG	AATTCCACCGCCC	6FAM-
		q25.3		6924		GGTAAAG	CAAAC	TTTCCGCCAAATATCT
								TTTCTTCTTCGCA-
								TAMRA
	RARRES1 3q25.31-	AC080013	66080-	Exon1	GGCGAGTCGGAT	CGCAAACTCCTAC	6FAM-
		3q26.1		66144		CGGAA	AACAAACGA	CGCGCGACGCTTCAC
								TTCTTCAA-TAMRA
	RASSF1 3p21.3	AC002481	18107 -	Exon1	ATTGAGTTGCGGG	ACACGCTCCAACC	6FAM-
				18171		AGTTGGT	GAATACG	CCCTTCCCAACGCGCC
								CA-TAMRA
	RBP1	3q23	AC046134 509 -598 Promoter/E	CGCGTTGGGAATT	GATACTACGCGAA	6FAM-
					xon1	TAGTTGTC	TAATAAACGACCC	ACGCCCTCCGAAAAC
								AAAAAACTCTACG-
								TAMRA
	RUNX3 1p36	AL023096	64646-	Exon2	CGTTCGATGGTGG	GACGAACAACGTC	6FAM-
				64762		ACGTGT	TTATTACAACGC	CGCACGAACTCGCCT
								ACGTAATCCG-TAMRA



  Supplemental Table5. Comparison of methylation levels of repetitive DNA elements between HCC cases with methylation and without methylation of the individual genes. 


		Meth (n=40)	30.8		1	13.4			100.2
	SOCS3	Unmeth (n=29)	24.0		0.530 13.2		0.731	70.3	0.653
	Gene	Meth (n=70)	LINE-1 25.6	P-	ALU 13.0		P-value SAT2 76.6	P-value
	SYK	Unmeth (n=64)	methylation 23.0	value 0.008 12.6 methylation	0.029	PMR 59.4	0.001
		Meth (n=35)	level (%) 29.0		level (%) 13.9		101.5
	APC TERT	Unmeth (n=41) Unmeth (n=90)	22.8 23.9		0.079 12.8 <0.00 13.0		0.542 0.539	68.4 69.1	0.443 0.010
		Meth (n=58) Meth (n=9)	26.7 36.5		1	13.2 13.6			78.6 123.1
	BCL2 Abbreviation: PMR, percent of methylated reference Unmeth (n=71) 24.1 0.131 12.7		0.072	75.9	0.757
		Meth (n=28)	27.7			13.9			71.4
	CACNA1G Unmeth (n=66)	27.0		0.013 13.5		0.042	82.2	0.078
		Meth (n=33)	21.3			12.2			57.6
	CALCA	Unmeth (n=69)	24.8		0.699 12.9		0.289	74.6	0.993
		Meth (n=30)	25.6			13.5			74.8
	CCND2	Unmeth (n=71)	23.1		0.003 13.0		0.813	67.5	0.054
		Meth (n=28)	30.1			13.2			96.1
	CDKN1C	Unmeth (n=49)	27.4		0.039 13.3		0.371	77.6	0.640
		Meth (n=50)	9 22.9	0.969 26.4	12.8	0.011 13.2	71.6	0.155 79.4	0.159
	CRABP1	Unmeth (n=52)	7.7 22.8		19.4 0.026 12.7		12.2 0.136	71.1	57.3 0.540
	Tumor size	Meth (n=47)	27.7			13.5			79.0
	<5.6 cm DLEC1	(n=49) Unmeth (n=21)	7.5 20.8	0.409 27.1 0.039 12.4	0.059 13.1 0.262	63.6	0.664 78.9 0.370	0.536
	>5.6 cm	(n=50) Meth (n=78)	8.1 26.3		23.0	13.2		12.9	77.7	70.9
	Histologic GRIN2B	Unmeth (n=81)	23.4		<0.00	12.9		0.403	69.1	0.043
	Grade	Meth (n=18)	32.7		1	13.6			104.3
	1, 2 GSTP1	(n=68) Unmeth (n=30)	7.9 23.4	0.243 24.6 0.295 12.8	0.725 13.2 0.556	66.3	0.470 65.8 0.428	0.095
	3, 4	(n=31) Meth (n=69)	6.9 25.9		25.5	13.2		12.7	77.8	91.1
	Associated HOXA1	Unmeth (n=24)	20.0		0.008 12.0		0.045	64.3	0.357
	liver condition Meth (n=75)	26.7			13.4			78.1
	LC NEUROG1 Unmeth (n=68) (n=66)	8.6 22.5	0.001 26.2 <0.00	13.2	0.146 13.2 0.619	69.2	0.253 62.1 0.200	0.210
	CH	(n=33) Meth (n=31)	6.1 30.8		22.8 1	12.8		12.5	87.1	55.9
	Abbreviations: PMR, percent of methylated reference; TNM, Tumor-Node-Metastasis; P16 Unmeth (n=48) 27.0 0.090 13.4 0.325 74.8 0.991
	LC, liver cirrhosis; CH, chronic hepatitis Meth (n=51) 23.3		12.8			74.6
	PTGS2	Unmeth (n=10)	16.2		0.006 11.9		0.179	50.4	0.177
		Meth (n=89)	26.1			13.2			77.8
	RUNX3	Unmeth (n=55)	23.4		0.088 12.6		0.110	67.6	0.210
		Meth (n=44)	27.2			13.6			84.0
	SFRP1	Unmeth (n=59)	21.2		<0.00 12.8		0.275	59.4	0.002
Supplemental Table 1. Primers and probes used for MethyLight assay SOCS3