Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models
Fig 6
Ovarian cancer mutation signature analysis.
a SNV mutation signatures. SNVs are organized according to the SNV type (color). Within each type, SNVs are further organized into the pattern of flanking nucleotides (A—A, A—C, …,T—G, T—T). b SV mutation signatures. SVs are grouped by type (DEL: deletion, DUP: tandem duplication, INV: inversion, FBI: foldback inversion, TR: translocation). c Heatmap of relative signature probabilities in ovarian cancer samples. Each heatmap column represents a single sample, and is composed of the SNV and SV signature probabilities output from the MMCTM model. The values for each signature (row) have been standardized, producing z-scores. Heatmap display has been truncated to ±3. Samples have been hierarchically clustered according to their transformed signature probabilities and cluster labels are indicated with colors underneath the dendrogram. The number of samples in each cluster is indicated in parentheses in the cluster legend. Samples from the ICGC OV-AU project are indicated with black bars, as is microsatellite instability (MSI) and gene mutation status. Samples with zero mutations for a mutation type also have greyed signature probability cells. The number of SNVs for a POLE mutant sample has been truncated to 40k in the barplot; The actual number is 596,135. d Annotation associations for sample clusters. Upward- and downward-pointing triangles indicate enrichment and depletion, respectively. Adjusted p-values >0.05 are not shown. Colors correspond to cluster colors indicated in the heatmap. e Kaplan-Meier curves for HGSC samples only. f Risk table for HGSC samples only. Kaplan-Meier curve plots and risk tables share x-axes. g Correlation heatmap between SNV and SV signatures.