Figure S5 from Intragenic Rearrangement Burden Associates with Immune Cell Infiltration and Response to Immune Checkpoint Blockade in Cancer

Figure S5. IGR burden correlates with tumor-infiltrating lymphocytes and pro-inflammatory pathways in WGS560 TNBC samples. (a) The distributions of IGR burden in TNBC subtypes. Wilcoxon rank sum tests were conducted to test if the median of IGR burdens in a certain subtype is significantly different than the other subtypes. `*` p<0.05. (b) Scatter plot revealing the association between HRD score (X-axis) and inflame signature (Y-axis), colored according to IGR burden. (c) Boxplots showing the distribution of inflaming signature, total mitoses and HRD score in IGRhigh and IGRlow tumors (samples outside the 10%-90% range are considered outliers). (d) Scatter plot showing the correlation between SCNA and HRD score (Pearson R=0.263, p=0.0008), and between SCNA and T-inflamed signature (Pearson R=-0.037, p=0.76) (e) The p-value for each marker in the multivariate model containing all markers including HRD and different types of genetic markers against T inflamed signature in TNBC tumors, when the confounding effects from other variables are removed. (f) Heatmap displays the normalized expression level of genes important in tumor immunology in TNBC samples. Samples are annotated by mitotic score, tumor grade, TIL and IGR level. (g) Enrichment plots for the pathways of interest as revealed by GSEA.