Extended Data Fig. 4: Subclonal SCNAs and T cell infiltration.
From: Using DNA sequencing data to quantify T cell fraction and therapy response
a, Overview of immune heterogeneity across multi-sample pan-cancer cohort with tumour samples ranked by TCRA T cell fraction, upper panel: histogram of entire cohort, lower panel: tumour sample grouped by patients with solid horizontal lines joining regions from the same patient, each line includes 2 or more tumour region and dashed red line is at the mean TCRA T cell fraction in the cohort (0.11). b, Overview of patients in the multi-sample pan-cancer cohort. c, Lower panel: number of tumours in pan-cancer multi-sample cohort with subclonal gains (dark red) or losses (dark blue) across the genome, horizontal lines signify the samples which have more than 30 tumours (Methods) with subclonal gains or losses. Upper panel: - log10(p-value) of the 160 cytoband regions tested for association between TCRA T cell fraction and subclonal gains (dark red points) or losses (dark blue points). Red horizontal line marks significance threshold, only one region is significant, a loss event on chromosome 12q24.31-32. d, Volcano plot for the RNA-seq analysis in the TRACERx100 cohort between samples with 12q24.31-32 loss and samples without, genes within the locus are labeled, dotted lines at fold change of 0.25 and adjusted P = 0.05.
