TCR and BCR gene segment expression analysis.

Expression levels of 353 BCR gene segments and 240 TCR gene segments were determined for TCGA bladder tumor samples with available TCGA mRNA-sequencing data and survival data using bedtools (version 2.17.0). Gene expression values were normalized to the upper quartile of total reads within a sample as previously described (35). Survival analyses were performed using a Cox PH model to derive P values and coefficients for each gene segment using the Cox PH function in the survival package in R. The number of gene segments that were significantly associated with improved survival (P < 0.05 and coefficient <0) was calculated for each bladder tumor subtype. Null distributions describing the expected number of prognostic gene segments for each subtype were estimated with 95% CIs according to the bootstrap method previously published by our group (15).

Fisher’s exact test was used to compare the number of BCR segments and TCR segments significantly associated with improved survival among all subtypes.