Identifying primary and secondary MLH1 epimutation carriers displaying low-level constitutional MLH1 methylation using droplet digital PCR and genome-wide DNA methylation profiling of colorectal cancers

Table 1 Overview of the sample composition and tumour characteristics within each of the four Consensus Clusters derived from genome-wide DNA methylation profiling of six CRC subtypes (reference groups)

	Consensus cluster 1	Consensus cluster 2	Consensus cluster 3	Consensus cluster 4
Number of CRCs	20	3	9	6
Age at CRC diagnosis (mean ± s.d)	38.7 ± 10.6	45.9 ± 12.8	65.5 ± 9.65	39.2 ± 11.3
MLH1 promoter methylation^a (mean ± s.d)	0.076 ± 0.02	0.082 ± 0.02	0.548 ± 0.089	0.761 ± 0.045
CIMP^b (% positive)	0 (0%)	1 (33%)	9 (100%)	0 (0%)
Mean methylation across the VM-CpGs^c	0.32	0.42	0.45	0.35
Lynch syndrome (n = 9)	8	1	0	0
MMR-proficient CRC (n = 9)	8	1	0	0
Double somatic MMR mutation CRC (n = 5)	4	1	0	0
Sporadic MLH1 methylated CRCs (n = 9)	0	0	9	0
MLH1 primary epimutation (n = 5)	0	0	0	4
MLH1 secondary epimutation (n = 1)	0	0	0	2

^aMean methylation (β-values) across the regulatory C region of MLH1
^bCIMP was determined by the methylation levels of CpG probes overlapping five previously defined genes [40]
^cMean methylation levels across the 77,113 most variably methylated CpGs (VM-CpGs), which was used for defining the Consensus Clusters. s.d.—standard deviation, VM-CpGs—(77,113) variably methylated CpGs defined by having high variation in the methylation patterns as ranked by standard deviation across 38 reference CRCs

ISSN: 1868-7083