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Table 2 Genome wide methylation profiling in HCC

From: DNA methylation: potential biomarker in Hepatocellular Carcinoma

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