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Background  DNA hypermethylation is reported as a frequent event and prognostic marker in head and neck squamous cell carcinomas (HNSCC). Methylation has been commonly assessed with non-quantitative methodologies, such as methylation-specific PCR (MSP). We investigated previously reported hypermethylated genes with quantitative methodology in oral tongue squamous cell carcinomas (OTSCC).    Results  The methylation status of 12 genes in 115 OTSCC samples was assessed by one or more of three quantitative analyses: methylation sensitive high resolution melting (MS-HRM), sensitive-melting analysis after real time-methylation specific PCR (SMART-MSP), and bisulfite pyrosequencing.  In contrast to much of the literature, either no or infrequent locus-specific methylation was identified by MS-HRM for  DAPK1 ,  RASSF1A ,  MGMT ,  MLH1 ,  APC, CDH1 ,  CDH13, BRCA1 ,  ERCC1 , and  ATM . The most frequently methylated loci were  RUNX3  (18/108 methylated) and  ABO  (22/107 methylated). Interrogation of the Cancer Genome Atlas (TCGA) HNSCC cohort confirmed the frequency of significant methylation for the loci investigated.  Heterogeneous methylation of  RUNX3  (18/108) and  ABO  (22/107) detected by MS-HRM, conferred significantly worse survival ( P  = 0.01, and  P  = 0.03). However, following quantification of methylation levels using pyrosequencing, only four tumors had significant quantities (>15%) of  RUNX3  methylation which correlated with a worse patient outcome ( P  <0.001), while the prognostic significance of  ABO  hypermethylation was lost.  RUNX3  methylation was not prognostic for the TCGA cohort ( P  = 0.76).    Conclusions  We demonstrated the critical need for quantification of methylation levels and its impact on correlative analyses. In OTSCC, we found little evidence of significant or frequent hypermethylation of many loci reported to be commonly methylated. It is likely that previous reports have overestimated the frequency of significant methylation events as a consequence of the use of non-quantitative methodology.    Electronic supplementary material  The online version of this article (doi:10.1186/1868-7083-6-22) contains supplementary material, which is available to authorized users.

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