Supplementary Figure S3 from The Landscape of Somatic Genetic Alterations in Metaplastic Breast Carcinomas

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<p>Supplementary Fig. S3. Patterns of copy number alterations in metaplastic breast cancers (MBCs) and triple-negative invasive ductal carcinomas of no special type (IDC-NSTs) and unsupervised clustering of metaplastic breast cancers (MBCs) and triple-negative IDC-NSTs based on copy number alterations and somatic mutations. Frequency plot and multi-Fisher's exact test comparisons of copy number gains and losses in (a) MBCs and triple-negative IDC-NSTs and in (b) MBCs of triple-negative phenotype and triple-negative IDC-NSTs, and frequency plot and multi-Fisher's exact test comparisons of high-level gains/ amplifications and deletions in (c) MBCs and triple-negative IDC-NSTs and in (d) MBCs of triple-negative phenotype and triple-negative IDC-NSTs. In each panel (a-d), the frequency of gains/ high-level gains/ amplifications (purple bars) or losses/ deletions (orange bars) for each gene is plotted on the y-axis, according to their genomic position on the x-axis. Inverse Log10 values of the Fisher's exact test p-values are plotted according to genomic location (x-axis). Hierarchical clustering of (e) copy number alterations of MBCs and triple-negative IDC-NSTs using categorical states (i.e. gains, losses, amplifications and homozygous deletions) using Euclidean distance metric and the Wards algorithm, and of (f) somatic non-synonymous mutations and (g) somatic likely pathogenic mutations in genes found in at least one of the cancer gene lists (29-31) or were more frequently mutated in MBCs than triple-negative IDC-NSTs using an asymmetric binary distance metric and complete-linkage hierarchical clustering. Sample types, types of copy number alterations and the presence of somatic mutation in a given gene are color-coded according to the color key.</p>