Fig. 2: Landscape of genomic alterations in 78 GISTs.

a Integrated plots of clinical and genomic alterations in 78 GISTs from 68 patients. The middle panel shows selected mutated genes and variant types. Known driver genes of GIST and recurrently mutated genes detected in at least 3 patients are included. The mutation frequency of each gene is shown as a bar plot on the left with the number of affected cases labeled in parentheses. The corresponding GO biological process for each gene are shown as colored blocks on the right. Blue annotations on the right indicate whether the genes are in the Cancer Gene Census (CGC) list. The bottom panel shows selected focal CNV genes detected by GISTIC2.0. The copy number: CN = 0 indicates a Deep Deletion, CN = 1 indicates a Shallow Deletion, CN = 3 indicates a Gain and ≥4 indicates an Amplification. The red gene symbols indicate known GIST drivers. b Bar plots illustrating relative proportion of recurrently mutated genes (top) and copy number alterations (bottom) by different risk. c Lollipop plots showing the distribution of all non-silent mutations in KIT, PDGFRA, and YLPM1. The scale bars represent the length (amino acids) of the protein sequence and the protein domains of the gene are indicated by colors. The number in parentheses denotes the number of patients. d 96-mutation spectrum of KIT mutations in GISTs. A total of 59 SNVs are identified in 46 GISTs. The distributions of KIT mutations are different from the overall SNV distributions, showing T > C and T > A bias. Source data are provided as a Source Data file.