Extended Data Fig. 3: Extended analysis on determinants of TCRA T cell fraction.
From: Using DNA sequencing data to quantify T cell fraction and therapy response
a, Association of blood TCRA T cell fraction to histology in TRACERx100 (n = 93 LUAD and LUSC patients). b, Predictors of blood TCRA T cell fraction in TCGA LUAD and LUSC cohort (left panel: n = 1017, middle panel: n = 976, right panel: n = 714). c, Overview of samples in the TCGA LUAD and LUSC cohort. d, Summary of mean TCRA T cell fraction in PNE cohort. e, Overview plot of PNE cohort containing multi-sample microdissected tissue paired with normal blood samples. f, Summary of linear model for predicting blood TCRA T cell fraction, PNE infiltration defined as TCRA T cell fraction > 0.001, ESCC = Oesophageal squamous cell carcinoma, HGD = high grade dysplasia. g, Linear model for TCRA T cell fraction in PNE samples from genomic factors. h, Association of microbial reads from Kraken with TCRA T cell fraction in tumour samples (n = 880). i, -Log10 p-values for 59 microbial species tested for association with TCRA T cell fraction in blood and tumour sample in LUAD and LUSC. Red line represents the significance threshold at P = 0.000423. j, The significant hit Willamsia in LUAD tumours, red dots represent samples where reads were detected while blue represent samples with no reads detected (n = 501). k, The significant hit Paeniclostridium in LUSC tumours (n = 379). All Wilcoxon tests refer to Wilcoxon rank-sum (Mann-Whitney U) tests and are two sided. Boxplots represent lower quartile, median and upper quartile.
