PAM diagnostic panel model for clear cell renal cell carcinoma. (A) ROC curve of best 4 CpG model (Benjamini and Hochberg-adjusted P = 1.46 × 10-20) from PAM diagnostic panel produced in the HudsonAlpha/Stanford data (ROC AUC = 0.990) and applied to TCGA (ROC AUC = 0.972). (B) DNA methylation at cg04511534, a CpG in the most predictive HudsonAlpha/Stanford model (Mann-Whitney test; Bonferroni-adjusted P = 0.2524 for HudsonAlpha/Stanford normal tissues versus TCGA normal tissues; Bonferroni-adjusted P = 0.1848 for HudsonAlpha/Stanford tumor tissues versus TCGA tumor tissues; Bonferroni-adjusted P <0.0001 for HudsonAlpha/Stanford normal tissues versus TCGA tumor tissues, Bonferroni-adjusted P <0.0001 for HudsonAlpha/Stanford tumor tissues versus TCGA normal tissues). (C) Expression of GGT6 in TCGA tumor and normal tissue data (Mann-Whitney test; P <0.0001). (D) GGT6 expression versus cg04511534 methylation in TCGA tumor tissue data (linear regression; P <0.0001, R2 = 0.5030). Random model is 50 random draws of 5 non-significant training set CpGs.