Low T cell diversity is associated with poor outcome in bladder cancer - Bulk TCRseq data

T cells are crucial effector cells in the endogenous defense against cancer, yet the clinical impact of their quantity, diversity, and dynamics remains underexplored. In this study we performed bulk TCRseq on tumor and serial blood samples from patients with muscle invasive (n patients = 119) or non-muscle invasive bladder cancer (n patients = 30). The goal was to investigate the clinical relevance of the blood and tumor TCR repertoire in patients with bladder cancer.

Type: Pooled Clone Sequencing
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

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Dataset ID	Description	Technology	Samples
EGAD50000001382	For this dataset we performed bulk TCRseq on tumor and serial blood samples from patients with muscle invasive bladder cancer (n patients = 119, n blood = 209, n tumor = 28) or non-muscle invasive bladder cancer (n patients = 30, n blood = 56, n tumor = 19) for a total of 149 patients and 312 samples. Each sample consists of a paired fastq file. Sequenced on the Ilumina NovaSeq6000 platform using SP and S1 flow cells (v1.5, 2x101 cycles), with a mean yield of 42 million reads covering the CDR3β region.	Illumina NovaSeq 6000	312

Publications	Citations
Low T cell diversity associates with poor outcome in bladder cancer: A comprehensive longitudinal analysis of the T cell receptor repertoire. Kjær A, Kristjánsdóttir N, Juul RI, Nordentoft I, Birkenkamp-Demtröder K, Ahrenfeldt J, Strandgaard T, Radif D, Hodgson D, Abbosh C, Aerts HJWL, Agerbæk M, Jensen JB, Birkbak NJ, Dyrskjøt L. Cell Rep Med 6: 2025 102101	2