Fig. 4: DNA alterations and DNA methylation patterns in ERpHER2n BC with respect to HRD status.
From: Homologous recombination deficiency in primary ER-positive and HER2-negative breast cancer
a Genome-wide frequency of copy number gain and loss in LumB tumors stratified by HRDetect status. b Bar plot of FDR-adjusted two-sided Wilcoxon’s test values (-log10 transformed) for four copy number signatures (CN) with an FDR-adjusted p < 0.05 between HR-proficient and HRD tumors stratified by PAM50 subtype. c Proportions of CN3, CN12, CN17, and CN23 in LumB tumors stratified by HRD status. Two-sided p-values were calculated using Wilcoxon’s test and adjusted for FDR. d Frequency of driver alterations in LumB tumors differs between HRD and HR-proficient tumors. Only genes with at least two affected tumors and a Fisher’s exact test two-sided p < 0.1 are shown. e Principal component analysis of tumor purity-adjusted DNA methylation data (beta values) based on the 5000 most variant distal-ATAC CpGs in LumB tumors. Black dots represent tumors with an HRDetect HRD classification. The first two principal components (PC1 and PC2) are shown. f Same as in E, but for CpGs in a proximal-ATAC context. g Same as in (e), but for CpGs in a promoter-ATAC CpG context. Boxplot elements correspond to: (i) center line = median, (ii) box limits = upper and lower quartiles, (iii) whiskers = 1.5x interquartile range. In violin plots, top axes indicate group sizes.
