Fig. 1

Identification of differential methylation of the TREX2 gene in laryngeal cancer. a Quantitative DNA methylation analysis using EpiTYPER assay in a cohort of 161 laryngeal cancer tumor tissues (T), 58 adjacent non-cancerous normal tissues (A), and 24 normal mucosa samples from non-cancer patients who underwent tonsillectomy (N). Average methylation data for EpiTYPER TREX2_2 amplicon (see Fig. 1b) are shown; the p value refers to ANOVA test across the three sample subsets. b Upper panel: map of the TREX2 gene locus with EpiTYPER PCR amplicons, single CpG dinucleotides analyzed in EpiTYPER (black), Illumina Infinium BeadChIP CpG probe locations (cg18879010 and cg 09364317), TREX2 transcript (blue), and CpG islands (green) indicated. Informative CpG unit 3.4 of TREX2_2 is marked with a red box. Lower panel: heat map showing EpiTYPER results for amplicons TREX2_1 and TREX2_2 in laryngeal cancer tumors (n = 58, red) and adjacent normal tissue controls (n = 25, green), with DNA methylation at individual CpGs depicted as a color gradient ranging from white (non-methylated) to orange (fully methylated). Corresponding EpiTYPER amplicons are listed above, and DNA methylation standard values (std) are shown below. Grey: data unavailable/excluded. c Methylation analysis of matched pairs of laryngeal tumor and adjacent tissue samples at the informative CpG unit 3.4 of the TREX2_2 amplicon; p value for two-tailed Student’s unpaired t test. d Average TREX2_2 methylation in colorectal cancer tumor tissues (T) and adjacent normal tissues (a). p value for two-tailed Student’s paired t test. Box-whisker plots show mean with 10 to 90 percentile