Fig. 3

Analytical Performance and Tumor Tissue Validation of Methylation-Based Models for Melanoma Detection. A Box and whisker Tukey plot comparing the Pan-Cancer with Melanoma Specificity score between control and melanoma samples. The boxes represent the interquartile range (IQR), with whiskers extending to 1.5 times the IQR. Outliers beyond this range are indicated as individual points. For both panels, we used 124 skin or lymph node samples from the EWAS dataset with no known diagnosis of cancer and 327 melanoma samples sourced from connective, subcutaneous, and other soft tissues, lymph nodes, or skin, also from the EWAS dataset. P-values between group pairs are shown on the plot. B ROC curve evaluating the performance of the Pan-Cancer with Melanoma Specificity Model in distinguishing control from melanoma samples. Sensitivity and specificity values were selected based on the highest likelihood ratio. The AUC value is shown in the figure. C Box and whisker Tukey plot comparing methylation levels between the same 124 control samples and 327 melanoma samples using the Melanoma Specific Model. The boxes represent the interquartile range (IQR), with whiskers extending to 1.5 times the IQR. Outliers beyond this range are indicated as individual points. Statistical significance between the groups is denoted by a p-value on the plot. D ROC curve evaluating the performance of the Melanoma Specific Model in distinguishing control from melanoma samples, with the remaining details the same as in the Pan-Cancer analysis. Sensitivity and specificity values were selected based on the highest likelihood ratio. The AUC value is shown in the figure. E and F The heatmaps represent the methylation levels of 35 individual CpG sites (F) and average methylation levels per gene (F) across cancer biopsy samples. Each row corresponds to a unique CpG site (E) or the average methylation level of all CpG sites within a gene (F), while each column represents a cancer biopsy sample. The samples include cancers from stages I–IV. The color intensity indicates the methylation status, with darker shades signifying higher methylation levels and cooler shades representing lower. This visual comparison allows for an in-depth assessment of methylation patterns both at the CpG site level and the gene level.