Table 2.
The characteristics of the six CRCs in the diagnostically challenging group comprised of carriers of MLH1 promoter VUS (n = 3) and MLH1 methylated early-onset CRCs (n = 3)
| Inclusion Group | Dx age (yrs) | Sex | CRC anatomical site | MMR IHC | MSIe | Mean methylation in the VM-CpGsd | CIMP in CRC (Total positive)b | Mean MLH1 promoter methylation (Tumour) a | Blood MLH1 promoter methylation (MethyLight)c |
Non-tumour MLH1 promoter methylation (ddPCR)d | Additional tissue tested (MethyLight)c | MMR genes LOH/somatic mutation | APC promoter methylationf | KRAS somatic mutation |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MLH1 VUS (MLH1: c.-11C > T) |
68 | F | Proximal | MLH1/PMS2 loss | MSI-H | 0.288 |
Negative (0/5) |
0.43 | 0% |
Blood—0% NMadj—2.3% NMdist—1.2% Buccal—6.5% |
– | MLH1 LOHg | 0.12 | None detected |
|
MLH1 VUS (MLH1: c.-11C > T) |
60 | M | Proximal | MLH1/PMS2 loss | MSI-H | 0.392 | Negative (2/5) | 0.39 | 1% |
Blood—4.5% NMadj—3.4% NMdist—nt Buccal—13.9% |
Duodenal cancer—29% | MLH1:p.S131Ter | 0.46 | p.G12D |
|
MLH1 VUS MLH1: c-[28A > G; 7C > T] |
35 | F | Proximal | MMRp (Incomplete loss of MLH1/PMS2) | MSS | 0.282 | Negative (1/5) | 0.14 | 0% |
Blood—0% NMadj—0% NMdist—0% Buccal—0% |
– | None detected | 0.14 | p.G12A |
| MLH1me EOCRC | 37 | F | Proximal | MLH1/PMS2 loss | MSI-H | 0.374 | Negative (2/5) | 0.34 | 0% |
Blood—0% NMadj—nt NMdist—0% Buccal—nt |
– | MLH1: p.S108AfsTer28 | 0.59 | p.G12D |
| MLH1me EOCRC | 43 | M | Proximal | MLH1/PMS2 loss | MSI-H | 0.338 | Negative (0/5) | 0.42 | 1% |
Blood—< 1% NMadj—nt NMdist—4.1% Buccal—2.4% |
TVA—49% | MLH1: p.X701_splice | 0.57 | None detected |
| MLH1me EOCRC | 31 | M | Proximal | MLH1/PMS2 loss | MSI-H | 0.353 | Negative (1/5) | 0.67 | 0% |
Blood—0% NMadj—nt NMdist—nt Buccal—0% |
– | MLH1 LOHg | 0.35 | None detected |
NMdist denotes distal normal mucosal samples derived from resection margin (i.e. non-adjacent), NMadj denotes normal mucosal samples derived from histologically normal mucosal samples adjacent to the tumour, TVA Tubulovillous Adenoma
aThe values indicate mean β-values estimated from 4 CpGs overlapping MLH1 promoter C region [39] derived from the HMEPIC data
bAs assessed from the HMEPIC
cAs assessed by MethyLight technique
dMean methylation levels across the 77,113 most variably methylated CpGs, which was used for defining the Consensus clusters
eEstimated using MANTIS
fMean methylation from 16 CpGs across the APC promoter c(hr3:112,072,926–11,207,395)
gLOH—loss of heterogygosity (across the MLH1 locus). The LOH plot is shown in Additional file 9: Fig. S8