 Intratumoral immunity heterogeneity is poorly characterised. Here the authors apply exome sequencing, transcriptome profiling and T-cell repertoire profiling to multiple loci of non-small cell lung cancer patients' biopsies and find high spatial immune heterogeneity with local mutational burden correlating with T-cell clonal expansion, but not with cytotoxicity. This article was authored by Qingzhu Jiao, Wei Yiwu, Yu Chiwang, and others.