Table 1.

Summary of major findings from previous literature

Category	Genes	Chromosome	Function	References	Testing method	Sample	Major findings
Tumor suppressor genes	RASSF1A	3p21.3	Ras-associated domain family	[25]	PCR in combination with melting curve analysis, sequencing, and restriction enzyme analysis	11 cell lines and 38 UMs	DNA methylation in 91% UM cell lines, and in 50% primary Ums, promoter methylation associated with UM metastasis
				[26]	Methylation-specific PCR	42 UMs and 8 UM cell lines (7 primary and 1 metastatic UM)	Promoter methylation of RASSF1A was detected in 35 of 42 tumors (83%)
				[27]	Methylation-specific PCR	20 UM samples	Methylation rate of RASSF1A was 70%
				[28]	QRT-PCR	UM-15 clone	Lack of RASSF1A expression and full methylation of the RASSF1A promoter region in the UM-15 cell line
	RASEF	9q21	Ras pathway	[29]	HRM and digestion analysis, RT-PCR	11 UM cell lines and 35 primary UMs	All the five RASEF-expressing cell lines contained an unmethylated promoter while hypermethylation of all CpGs within the amplicon was present in all the six cell lines that lacked RASEF expression. There was a correlation between methylation and expression of RASEF in the primary tumor samples, but not as obvious as in the cell lines
	ITGA7/NDRG2/PITX2	12q13.2/14q11.2/4q25	Tumorigenesis	[30]	Bisulfite sequencing validation	63 cases of human UM	Promoter hypermethylation was extensively observed in these genes (85% methylated samples) in UM
	RAB31	18p11.22	Ras oncogene family	[31]	Methylation-specific PCR	67 UMs	Differential methylation between normal uvea and UM
	BAP1	3p21.1	Ubiquitin C-terminal hydrolases	[32]	Illumina infinium HM450 array	80 UMs	M3 developed initially followed by alterations of BAP1, which has distinct global DNA methylation from that observed in D3
Gylin-dependent kinase	p16INK4a	9p21	Stabilizer of the tumor suppressor protein	[33]	Methylation-specific PCR	12 UM cell lines and 22 UMs	Promoter is hypermethylated in 6 of 12 UM cell lines and in 7 of 22 primary UMs
Other genes	TIMP3	22q12.3	Extracellular matrix degradation	[34]	Microarray analysis and demethylation test	UM cell lines and 2 metastatic samples	5-fold decreased expression of TIMP3 in the metastatic cell lines
	PRAME	22q11.22	Encodes an antigen preferably expressed in human melanoma	[35]	Methylation probes in Methyl450K array	678 UM patients	12 CpG sites within and near the PRAME promoter region were hypomethylated in PRAME+ tumors
	hTERT	5p15.33	Telomerase reverse transcriptase	[36]	Methylation-sensitive single-strand conformation analysis and dot-blot assay	23 primary UMs	hTERT promoter methylation was found with a relatively high frequency (52%)
	EFS	14q11.2	CAS protein family	[37]	PCR	16 UMs	Full methylation of the EFS CpG island in 8 (50%), no methylation in 5 (31%), and partial methylation in 3 (19%) UMs
	DSS1	7q21.3–q22.1	DSB repair	[38]	Methylation-specific PCR	130 cutaneous melanomas, 64 UMs, 82 mucosal melanomas, and 75 SCC samples	There was an inverse correlation between DSS1 expression and methylation status of the promoter

CpG: C–phosphate–G; HRM: High-resolution melting-curve; PCR: Polymerase chain reaction; QRT-PCR: Quantitative real-time polymerase chain reaction; RT-PCR: Real-time polymerase chain reaction; SCC: Squamous cell carcinomas; UMs: Uveal melanomas; CAS: Cellular apoptosis susceptibility; DSB: DNA double-strand break; RASEF: Ras and EF-hand domain containing; EFS: Embryonal fyn-associated substrate; DSS1: Deleted in Split-Hand/Split-Foot 1; PRAME: Melanoma antigen preferentially expressed in tumors; TIMP3: Tissue inhibitor of metalloproteinases 3; BAP1: BRCA1 associated protein-1; ITGA7: Integrin alpha 7 subunit; NDRG2: N-myc downstream-regulated gene 2; PITX2: Paired-like homeodomain 2.