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Table 3 Summary of methylation events for each locus assessed by methylation sensitive high resolution melting (MS-HRM), and assessed in the Cancer Genome Atlas (TCGA) cohort a

From: Quantitative methodology is critical for assessing DNA methylation and impacts on correlation with patient outcome

Gene Total number of samples Level of methylation TCGA HNSCC(n = 305) TCGA OTSCC(n = 86)
0% <10% 10 to 25% 25 to 50% >50% Heterogeneous β-value >0.2 β-value >0.2
ABO 107 78 (73%) 7 (7%) 3 (3%) 0 0 19 (17%) 139 (46%) 32 (37%)
cg13506600, cg07241568
APC 105 102 (97%) 0 0 3 (3%) 0 0 50 (16%) 12 (14%)
cg14479889, cg03667968, cg16970232
ATM 48 48 (100%) 0 0 0 0 0 0 0
cg18457775, cg06750635
BRCA1 45 44 (98%) 1 (2%) 0 0 0 0 0 0
cg20187250, cg15419295, cg16963062, cg16630982, cg21253966, cg04110421, cg04658354
CDH1 114 91 (80%) 10 (9%) 0 0 0 13 (11%) 1 (0%) 1 (0%)
cg16739895, cg23989635, cg11255163
CDH13 111 107 (96%) 1 (1%) 0 0 0 3 (3%) 41 (13%) 9 (10%)
cg08747377
CDKN2A[96] 113 78 (69%) 15 (13%) 8 (7%) 6 (5%) 6 (5%) 0 55 (18%) 21 (24%)
cg04026675, cg13601799
DAPK1 91 87 (96%) 4 (4%) 0 0 0 0 46 (15%) 8 (9%)
cg08797471, cg13932603
ERCC1 47 47 (100%) 0 0 0 0 0 11 (4%) 3 (3%)
cg20467502, cg23902435
MGMT 50 37 (74%) 13 (26%) 0 0 0 0 23 (8%) 5 (6%)
cg02941816, cg05068430
MLH1 49 49 (100%) 0 0 0 0 0 1 (0%) 0
cg23658326
RASSF1A 49 48 (98%) 1 (2%) 0 0 0 0 11 (4%) 0
cg04743654, cg27569446
RUNX3 108 90 (83%) 0 0 0 0 18 (17%) 37 (12%) 16 (19%)
cg19590532, cg06377278          
  1. The frequency of methylation events assessed by MS-HRM is presented with the frequency of methylation events (β-value >0.2) for the TCGA HNSCC cohort and TCGA OTSCC subgroup. The Cg number of the probes from the Infinium HumanMethylation450 beadchip array that were examined in reference to the MS-HRM amplicons is annotated for each gene as ‘cg locus number’.
  2. TCGA HNSCC, The Cancer Genome Atlas head and neck squamous cell carcinoma cohort; TCGA OTSCC, The Cancer Genome Atlas oral tongue squamous cell carcinoma cohort.