Fig. 3

Somatic copy number alteration (SCNA) clustering and molecular subtypes. a Hierarchical clustering using the copy number profiles of focal regions from GISTIC2. Right bars indicate significant peak regions (7p22.3, 1q21.2, 13q14.2, and 12q14.1) from GISTIC2. Bottom panel: significantly mutated genes mentioned previously (TP53, ATRX, PTEN, and MSH family); copy number alterations in CDK4 (red) or RB1 (blue); gene expression profiles with DNA mismatch repair genes (MSH2, MSH3, MSH6, and PMS2) and PDGFRA; patient tumor status; cluster with SCNA status. P-values were calculated by Fisher’s exact test. b Comparison with copy number values of CDK4/RB1 in focal regions from CKSs and TCGA data. Red dots indicate patients with CDK4 amplification (copy number values > 2) and blue dots indicate patients with RB1 deletion (copy number values < − 1.2). P-values were calculated by t-test