DNA methylation: potential biomarker in Hepatocellular Carcinoma

Biomarker Research

Table 2 Genome wide methylation profiling in HCC

Promoter microarray
Discovery method	HCC patients (n)	Validation method	Validated genes	Publication	Year
MCAM-chip	10	Pyrosequencing	RASSF1A, p16, TBX4, MMP14, GNA14, SLC16A5, CCNA1	Gao et al. [36]	2008
	16	Pyrosequencing	KLHL35, PAX5, PENK, SPDYA, LINE-1	Shitani et al. [40]	2012
DMH-chip	21	MSP	KLK10, OXGR1	Lu et al. [37]	2008
MeDIP-chip	6	MassArray	CYP24A1, DLX1, ZNF141, RASGRF2, ZNF382, TUBB6, NPR1, RRAD, RUNX3, LOX, JAKMIP1, SFRP4, DUSP4, PARQ8, CYP7B1	Deng et al. [38]	2010
	11	Pyrosequencing	AKR1B10, CENPH, MMP9, MMP12, PAGE4, S100A5, MMP2, NUPR1	Stefanska et al. [39]	2011
Beadarray
Discovery method	HCC patients (n)	Validation method	Validated genes	Publication	Year
GoldenGate	20	Methylight assay	APC	Archer et al. [49]	2010
	38	Pyrosequencing	RASSF1, GSTP1, APC, GABRA5, LINE-1	Hernandez-Vargas et al. [43]	2010
	45	Bisulfite sequencing	ERG, HOXA9	Hou et al. [47]	2013
Infinium 27K	3	COBRA and bisulfite sequencing	WNK2, EMILIN2, TLX3, TM6SF1, TRIM58, HIST1H4F, GRASP	Tao et al. [44]	2011
	62	NIL	NIL	Yang et al. [118]	2011
	13	NIL	NIL	Ammerpohl et al. [48]	2012
	62	Pyrosequencing	CDKL2, STEAP4, HIST1H3G, CDKN2A, ZNF154	Shen et al. [42]	2012
	63	Pyrosequencing	PER3	Neumann et al. [50]	2012
	71	Pyrosequencing	NEFH, SMPD3	Revill et al. [53]	2013
Infinium 450K	66	NIL	NIL	Shen et al. [46]	2013
	27	Pyrosequencing	GSTP1, RASSF1, BMP4, DLGAP1, GPR35	Song et al. [45]	2013
	6	Bisulfite sequencing	DBX2, THY1	Zhang et.al. [41]	2013

COBRA, Combined bisulfite restriction analysis; MSP, Methylation specific PCR.

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