Genome-wide gene frequencies of APOLLOH predictions, copy number profiles from the current 23 cases, and an external (METABRIC) data set (Curtis et al. 2012), and monoallelic expression. From top to bottom, the first and second panels show copy number profiles for cohorts of 118 basal-like subtype breast cancer patients from METABRIC, analyzed on Affymetrix SNP6.0 arrays, and the 23 TNBC patients. Deletion gene frequency profiles (negated for display purposes) in both data sets show similar patterns to deletion LOH frequencies shown in the third panel. The fourth and fifth panels, respectively, show the profile of genes affected by copy neutral LOH and the profile of overall LOH events including genes found within deletions, copy neutral regions, and amplifications. The last panel shows the frequency profile of genes that are observed with monoallelic expression (MAE) as a consequence of genomic LOH events for 22 samples with available RNA-seq data.
