Table 1.

Prognostic and predictive DNA methylation biomarkers for colorectal cancer.

Gene /panel	Material	Cancer samples	Stage	Effect of methylation	Survival / Response	Method	Ref
APC1A, CDKN2A, RASSF1A	Tissue	111	I-IV	Poor survival	^*RR = 2.20, P = .037	Pyrosequencing	[174]
AGBL4, FLI1, TWIST1	Plasma	353	I-IV	Poor DFS	HR= 2.00, P = .001	MALDI-TOF	[175]
AGBL4, FLI1, TWIST1					^*HR = 0.495, P = .495
CDKN2A	Tissue	902	I-IV	Poor OS	HR = 1.36, P = .004	qMSP	[176]
					^*HR = 1.03, P = .78
CDKN2A	Tissue	111	I-IV	Poor survival	P = .036	Pyrosequencing	[174]
					^*P = .065
CDKN2A, KRAS mut	Tissue	86	I-III	Poor OS	^*HR = 3.0, P = .036	MSP	[177]
CDKN2A, NEUROG	Tissue	497 (FOLFOX)	II-III	Worse OS	^*HR = 2.89, P = .002	qMSP	[178]
CDX2	Tissue	72	I-IV	Poor OS	^*HR = 3.02, P = .030	MSP	[179]
CIMP	Tissue	1035	I-IV	Poor OS	^*HR = 1.89, P < .001	qMSP	[39]
				Poor TTR	^*HR = 1.86, P < .001
CIMP	Tissue	206	I-IV	Poor OS	P = .029	qMSP	[33]
					^*CIMP not included
CIMP	Tissue	734	I-IV	Poor OS	P = .009, ^*P = .451	qMSP	[34]
				Poor DFS	P = .008, ^*P = .337
CIMP	Tissue	190 (cohort 1)	I-IV	Poor CSS	^*HR = 1.84, P > .05	qMSP	[35]
		574 (cohort 2)			^*HR = 1.10, P > .05
CIMP	Tissue	272 (MSS)	I-IV	Poor relative survival	^*HR = 2.90, P = .001	MSP	[36]
CIMP	Tissue	649	I-IV	Improved CSS	^*HR = 0.44, P < .05	qMSP	[32]
CIMP	Tissue	24 (CIMP+)	II-III	5-FU improved survival	P = .022	qMSP	[40]
		100 (CIMP−)		5-FU no survival benefit	P = .988
CIMP	Tissue	67 (CIMP+)	III	5-FU improved survival	P = .002	MSP	[41]
		140 (CIMP−)		5-FU no survival benefit	P = .60
CIMP	Tissue	615	III	Poor OS	HR = 1.36, P = .044	qMSP	[42]
					^*P = .031
CIMP	Tissue	145 (CIMP+)	III	IFL (vs 5-FU/LV) improved OS	HR = 0.62, P = .07	qMSP	[42]
		470 (CIMP−)		IFL (vs FU/LV) worse OS	HR = 1.38, P = .049
CIMP	Tissue	12 (CIMP+)	II-III	5-FU worse DFS	P = .023	MSP	[46]
		38 (CIMP−)		5-FU no survival benefit	P = .146
CIMP/MLH1	Tissue	115	II	Poor DFS	^*HR = 3.16, P = .011	qMSP	[180]
				Poor OS	^*HR = 4.70, P = .002
CREB1	Tissue	33 (rectum)	II-III	Predictive of lower response to radiation	P = .031(histology)	qMSP	[181]
DIRAS1	Tissue	146	I-IV	Poor OS	P = .012	MSP	[182]
FOXE1	Tissue	396	I-IV	Poor OS	P = .008	Illumina HM450	[183]
HLTF	Serum	103	IV	Poor OS	^*HR = 1.8, P = .04	qMSP	[49]
HLTF	Serum	77	I-IV	Poor OS	RR = 3.0, P = .008	qMSP	[184]
HOPX	Tissue	170	III	Poor DSS	^*HR = 1.40, P = .035	qMSP	[185]
HPP1	Plasma	467	IV	Poor OS	HR = 1.86, P < .05	qMSP	[48]
HPP1	Plasma (after therapy initiated)	467	IV	Predictive of non-responders to bevacizumab comb therapy	AUC = 0.77, NPV = 97.7 (RECIST)	qMSP	[48]
HPP1	Serum	103	IV	Poor OS	^*HR = 1.6, P < .05	qMSP	[49]
HPP1	Serum	77	I-IV	Poor OS	RR = 5.1, P = .001	qMSP	[184]
HPP1, HLTF	Serum	77	I-IV	Poor OS	^*RR = 3.4, P = .007	qMSP	[184]
IGFBP3	Tissue	34 (training)	II	Improved RFS	^*HR = 6.46, P = .012	qMSP	[186]
		81 (validation)			^*HR = 2.40, P = .029
IGFBP3	Tissue	425	II-III	Improved DFS	^*HR = 0.49, P < .01	Pyrosequencing	[47]
IGFBP3	Tissue	89 (methylated)	II-III	Chemotherapy no survival benefit	P = .20	Pyrosequencing	[47]
		157 (unmethylated)		Chemotherapy survival benefit	P = .040
KISS1	Tissue	100 (validation 1)	I-III	Poor DSS and OS	P = .034 (DSS), P = .015 (OS)	MSP, BGS	[187]
		190 (validation 2)			P = .030 (DSS)
MGMT	Plasma	49 (TMZ)	IV	Improved PFS	P = .008	MethylBEAMing	[53]
MGMT	Tissue	68	IV	Improved response to dacarbazine	DCR = 44% (methylated), DCR = 6% (unmethylated), P = .012	MSP	[188]
MGMT	Tissue	61 (training)	IV	Improved response to alkylating agents	PPV = 0.67, NPV = 0.89 (RECIST)	MethylBEAMing	[53]
		21 (validation)		Improved response to alkylating agents	PPV = 0.5, NPV = 0.67 (RECIST)
MGMT	Tissue	111	I-IV	Improved survival	^*RR = .36, P = .023	Pyrosequencing	[174]
MLH1	Tissue	195	I-IV	Improved OS	^*HR = .56, P = .01	MS-MLPA	[189]
PCDH10, SPARC, UCHL1	Tissue	71 (5-FU/LV)	II	Poor DFS and OS	P = .069 (DFS), P = .139 (OS)	qMSP	[190]
PCDH10, SPARC, UCHL1		72 (surveillance)		Improved DFS and OS	P = .031 (DFS), P = .003 (OS)
RARb2	Tissue	73	I-IV	Poor OS	P = .026	MSP	[191]
RET	Tissue	233 (series 1)	II	Poor OS	^*HR = 2.46, P < .05	MSP, pyrosequencing	[192]
		231 (series 2)			^*HR = 1.13, P > .05
		294 (series 3)			^*HR = 1.91, P < .05
SEPT9	Serum (after 1y follow-up)	137	II-III	Poor CSS	^*HR = 2.69, P < .05	qMSP	[193]
SFRP2	Tissue	77	I-IV	Poor OS	^*HR = 5.15, P = .041	MSP	[194]
SHISA3	Tissue	120 (OS)	I-IV	Poor OS	^*HR = 2.9, P = .002	Pyrosequencing	[195]
		83 (DFS)	II-III	Poor DFS	^*HR = 4.0, P = .003
SLFN11	Tissue	128	T1-T4/N0-N2	Poor OS	^*HR = 0.44, P = .022	MSP	[196]
			T1-T4/N0-N2	Poor RFS	^*HR = 0.44, P = .023
SYK	Tissue	139	I-IV	Poor OS	^*HR = 1.77, P = .001	MSP	[197]
SYNPO2	Tissue	31 (training)	I-IV	Poor DSS and OS	P = 0.132 (DSS)	MSP, BGS	[198]
		100 (validation 1)	II		P = .046 (DSS), P = .031 (OS)
		48 (validation 2)	II-III		P = .012 (DSS), P = .009 (OS)
TAC1	Serum (after 6 months follow-up)	144	II-III	Poor CSS	^*HR = 4.12, P ≤ .001	qMSP	[193]
	Serum (after 6 months follow-up)			Poor DFS	^*HR = 5.72, P < .001
TFAP2E	Tissue	74 (cohort I)	IV	Lower response to 5-FU	P < .001 (RECIST)	qMSP	[51]
		36 (cohort II)	IV		P < .001 (RECIST)
		42 (cohort III)			P < .001 (histology)
		68 (cohort IV)			P < .001 (histology)
TFAP2E	Tissue	193	I-III	Improved OS	^*HR = 2.24, P = .025	MS-HRM	[199]
				Improved RFS	^*HR = 2.44, P = .025
TFAP2E	Tissue	154 (chemotherapy)	II-III	Improved OS	^*HR = 2.55, P = .017	MS-HRM	[199]
				Improved RFS	^*HR = 2.36, P = .032
WNT5A	Tissue	126 (treated with 5-FU)	I-IV	Improved PFS	P < .005	MSP	[52]
WRN	Tissue	88 (treated with irinotecan)	NA	Improved OS	P < .001	MSP	[200]

Abbreviations: BGS, bisulfite genomic sequencing; COBRA, combined bisulfite restriction analysis; DCR, disease control rate (= partial response+ stable disease); DFS, disease free survival; DSS, disease specific survival; HR, hazard ratio; MSP, methylation specific PCR; MSS, microsatellite stable; NA, not available; NPV. Negative predictive value; OS, overall survival; PFS, progression free survival; PPV, positive predictive value; qMSP, quantitative methylation specific PCR; RECIST, response evaluation criteria in solid tumors; RFS, recurrence/relapse-free survival; RR, relative risk; TTR, time to recurrence.

Multivariate.