Mutations in CIC, NOTCH1 and FUBP1 were very significantly associated with high CGI methylation in LGG (P = 5.7 × 10−11, 5.2 × 10−7 and 9.9 × 10−5, respectively), mutation in PIK3CA was so in STAD (P = 7.4 × 10−9), and mutations in PTEN and PIK3R1 were so in UCEC (P = 5.9 × 10−7 and 1.6 × 10−4, respectively). Here, PIK3R1 is linked to gastric adenocarcinoma.