Fig. 5: Genomic landscape of PDxOs compared to PDXs and human tumors.
a, Correlation heat map illustrating genome-wide DNA methylation analysis for 11 sets of patient-derived models compared to commonly used breast cancer cell lines. The color scale indicates the Pearson correlation coefficient. b, Eleven sets of models were characterized at different time points (early and late) to assess molecular fidelity with the human tumors. The heat map is divided into four sections from top to bottom: annotations, exome sequencing variant detection, CN correlations from SNP array data and RNA-seq gene expression correlations. Mutation variants are shown with an oncoprint plot highlighting single-nucleotide variants and indels for commonly mutated genes in breast cancer. Quantitative CNV correlations are shown using a heat map of Spearman correlations for gene-level log2 CN ratios. Quantitative transcriptome correlations are shown using a heat map of Spearman correlations for gene-level log10-transformed RNA-Seq by Expectation-Maximization (RSEM) count estimates; NA, not applicable. c, Unsupervised clustering of the same models shown in b, with the PAM50 gene set to classify subtype.
