Fig. 2

Somatic copy number variants and structural variants. a Somatic copy number profile of the IBC cohort. X-axis represents genome coordinates ordered by chromosomes. Y-axis shows the frequency of copy number gain (red) and copy number loss (blue) in 1 Mb-length bins across the genome in IBCs. b Significance of differences of copy number profiles between IBC and non-IBC cohorts. X-axis shows genome coordinates by chromosome and the Y-axis shows the log-transformed p-value from the Fisher’s exact test, obtained from the comparison of frequencies of copy number gain (pink) and copy number loss (light blue) events between two cohorts. Dashed lines represent p-value = 0.01. All significant peaks (Bonferroni-adjusted p-value < 0.01) have less frequency in IBC, for both copy number loss and gain events. c Number of somatic SVs in individual IBC and non-IBC samples. Shades represent the types of somatic SVs. d Fractions of each type of somatic SVs in IBC and non-IBC cohorts. Each dot represents a sample color-coded by its ER status. P-values were calculated by Wilcoxon test and adjusted by Bonferroni method