Figure 4

Validation of human papillomavirus-positive (HPV+) and HPV-negative (HPV-) methylation signature. (A-C) Validation of consistency of t-statistics between formalin-fixed, paraffin wax-embedded (FFPE) and (A) fresh-frozen (FF) samples, (B) FF control probes and (C) HPV+ against HPV- cell lines. (D) Heatmap representation of signature of consistent hypermethylated methylation variable positions (hyper-MVPs; top) and hypomethylated MVPs (hypo-MVPs; bottom) in the Infinium DNA-methylation data. The DNA-methylation (β) values are represented using a color scale from yellow (low DNA methylation) to blue (high DNA methylation) normalized across each MVP. The HPV+ head and neck squamous cell cancer (HNSCC) methylation signature contains 2,194 consistent hyper-MVPs and 74 consistent hypo-MVPs across all three datasets. The six HNSCC cell-line samples were run in duplicate.