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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.