Supplementary Figure S2 from The Landscape of Somatic Genetic Alterations in Metaplastic Breast Carcinomas

Abstract

<p>Supplementary Fig. S2. Repertoire of somatic non-synonymous mutations of metaplastic breast cancers (MBCs) and triple-negative invasive ductal carcinomas of no special type (IDC-NSTs). Clinico-pathologic and immunohistochemical features, and non-synonymous somatic mutations somatic mutations identified in (a) 35 MBCs subjected to whole-exome sequencing, and in 69 triple-negative IDC-NSTs from TCGA breast cancer study (9) and in (b) 16, ten and nine chondroid, spindle and squamous MBCs, respectively, subjected to whole-exome sequencing. The effects of the mutations are colored-coded according to the legend, with hotspots colored in red. Mutations of indeterminate pathogenicity and likely passenger mutations are indicated by hatched boxes. The presence of multiple non-synonymous mutations in the same gene is represented by an asterisk. For MBCs, the presence of loss of heterozygosity of the wild-type allele of a mutated gene is represented by a diagonal bar, and mutations found to be clonal by ABSOLUTE (24) are indicated by a black box. Only recurrently mutated genes are presented (i.e. genes affected by non-synonymous somatic mutations in {greater than or equal to}2 MBCs). Gene names highlighted in purple were (a) significantly more frequently altered in MBCs or (b) differentially altered in the given subtype of MBC. Percentages to the right of the mutation heatmaps indicate the percentage of cases affected by non-synonymous somatic mutations in a given gene. Bar charts (top) indicate the number of non-synonymous and synonymous somatic single nucleotide variants (SNVs), and the number of somatic insertions and deletions (indels) for each sample. The dominant mutational signatures (35, 36) were assigned using deconstructSigs (37). Large-scale transitions (LST)-high and LST-low status was determined in accordance with Popova et al (39). TCGA, The Cancer Genome Atlas.</p>