Quantification of DNA methylation for carcinogenic risk estimation in patients with non-alcoholic steatohepatitis

Clinical Epigenetics

Table 2 The 21 CpG sites for which receiver operating characteristic curve analysis showed area under the curve (AUC) values larger than 0.95 for discrimination of non-cancerous liver tissue samples showing non-alcoholic steatohepatitis (NASH) from partial hepatectomy specimens from patients with hepatocellular carcinoma (HCC) (NASH-W) from normal liver tissue samples (NLT), and larger than 85% specificity for discrimination of NASH-W samples from non-cancerous liver tissue samples showing NASH from biopsy specimens from patients with morbid obesity but without HCC (NASH-O)

Probe ID^a	Gene symbol^b	Gene region^c	CpG type^d	Discrimination of NASH-W from NLT		Discrimination of NASH-W from NASH-O
Probe ID^a	Gene symbol^b	Gene region^c	CpG type^d	AUC	DNA methylation status^e	Specificity^f
cg00431813	C7orf50	Gene body	S_shelf/N_shore	0.960	NASH-W > NLT	0.978
cg05393736	NRBF2	TSS1500	N_shore	0.960	NASH-W > NLT	0.956
cg09580822	N/A			0.974	NASH-W < NLT	0.945
cg11820154	N/A			0.953	NASH-W > NLT	0.945
cg14950303	FOXD4L1	TSS1500	N_shore/N_shelf	0.957	NASH-W > NLT	0.912
cg15050398	LOC401242	Gene body	N_shelf	0.958	NASH-W < NLT	0.912
cg23785719	STK17A	TSS200	N_shore	0.962	NASH-W > NLT	0.912
cg26583598	ZSWIM6	Gene body		0.953	NASH-W > NLT	0.901
cg18210511	ZC3H3	Gene body	Island	0.956	NASH-W > NLT	0.901
cg05861743	APOM	Gene body	N_shelf/S_shelf	0.951	NASH-W > NLT	0.890
cg14288091	NIPAL2	Gene body/1st intron	N_shore	0.952	NASH-W < NLT	0.890
cg26385097	N/A			0.953	NASH-W < NLT	0.890
cg22083325	LOC440461	TSS200	N_shelf/Island	0.982	NASH-W > NLT	0.889
cg09580859	ZC3H3	Gene body	Island	0.951	NASH-W > NLT	0.879
cg13719443	LOC285847	Gene body	S_shore	0.952	NASH-W < NLT	0.879
cg26894854	SLC45A3	Gene body	N_shore	0.968	NASH-W > NLT	0.879
cg04662828	N/A			0.963	NASH-W < NLT	0.868
cg11152384	N/A			0.957	NASH-W < NLT	0.867
cg08912801	N/A			0.974	NASH-W < NLT	0.857
cg16319310	N/A			0.987	NASH-W < NLT	0.857
cg19861632	GPR125	Gene body		0.963	NASH-W > NLT	0.857

^aProbe ID of the Infinium HumanMethylation450 BeadChip
^bNational Center for Biotechnology Information (NCBI) database (Genome Build 37)
^cTSS1500 (from 200 bp upstream of the transcription start site [TSS] to 1500 bp upstream of it), TSS200 (from TSS to 200 bp upstream of it), 1st intron and gene body (2nd exon and downstream) were identified based on the RefSeq database (http://www.ncbi.nlm.nih.gov/refseq/)
^dCpG islands, island shores (2000-bp regions adjacent to a CpG island) and island shelves (2000-bp regions adjacent to an island shore) were identified based on the University of California, Santa Cruz (UCSC) genome browser (https://genome.ucsc.edu/)
^eNASH-W < NLT: the sample was predicted to be NASH-W and/or carcinogenic risk-positive when its DNA methylation level was lower than the cutoff value; NASH-W > NLT: the sample was predicted to be NASH-W and/or carcinogenic risk-positive when its DNA methylation level was higher than the cutoff value
^fSpecificity was defined as the ratio of the number of tissue samples not diagnosed as NASH-W based on the criteria relative to the exact number of NASH-O samples. N/A, not annotated (designed in the intergenic regions)

ISSN: 1868-7083