Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models
Fig 5
BRCA-EU 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, TR: translocation). c Heatmap of relative signature probabilities in BRCA-EU 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. ER, PR, and HER2 positive status, BRCA1/2 mutation or methylation status, other gene driver mutation status, HRDetect prediction, and MMRD status is indicated with black bars. Grey cells represent missing data for annotation tracks. Samples with zero mutations for a mutation type also have grey signature probability cells. d Correlation heatmap between SNV and SV signatures. e 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.