ArticleBriefings in bioinformatics2023
Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing.
Article in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 16 citations in OpenAlex.
- T cell immunomonitoring: a comparative analysis of traditional and novel methods to quantify and characterize human antigen-specific T cells.Nature protocols · 2026Review
- Cross-species molecular stratification enables T cell receptor diagnosis of Parkinson's disease.Genome medicine · 2026Article
- The case for caution in the application of whole-exome sequencing data for immune repertoire analysis.Briefings in bioinformatics · 2026Article
- Mapping the TCR landscape: computational tools empowering translational immunology and therapy design.Journal for immunotherapy of cancer · 2026Review
- SatTCR: a pipeline for performing saturation analysis of the T cell receptor repertoire and a case study of a healthy canine.MethodsX · 2026Article
- Single-Cell Multi-Tissue T Cell Clonal Dynamics Reveal Distinct Immune Coercion Landscapes in MSI and MSS Colorectal Cancer.International journal of molecular sciences · 2026Article
- A reproducible pipeline for TCR β-chain repertoire analysis from thoracic tumour RNA-seq and ICI-associated cardiac immunotoxicity.Frontiers in immunology · 2026Article
- The protective role of γδ T cells in endometrial cancer.Cancer immunology, immunotherapy : CII · 2025Article
- Informatics at the Frontier of Cancer Research.Cancer research · 2025Review
- Informatics at the Frontier of Cancer Research.Cancer research · 2025Review
- RNA-seq based T cell repertoire extraction compared with TCR-seq.Oxford open immunology · 2025Article
- A review on trends in development and translation of omics signatures in cancer.Computational and structural biotechnology journal · 2024Review
- γδ T-cells in human malignancies: insights from single-cell studies and analytical considerations.Frontiers in immunology · 2024Review
- Loss of TET2 increases B-1 cell number and IgM production while limiting CDR3 diversity.Frontiers in immunology · 2024Article
- Development and characterization of human T-cell receptor (TCR) alpha and beta clones' library as biological standards and resources for TCR sequencing and engineering.Biology methods & protocols · 2024Article
- Pulmonary microbiome and transcriptome signatures reveal distinct pathobiologic states associated with mortality in two cohorts of pediatric stem cell transplant patients.medRxiv : the preprint server for health sciences · 2023Article
- Comment on 'rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing'.Briefings in bioinformatics · 2023Article
- Intratumoral T-cell and B-cell receptor architecture associates with distinct immune tumor microenvironment features and clinical outcomes of anti-PD-1/L1 immunotherapy.Journal for immunotherapy of cancer · 2023Article
- Features of the TCR repertoire associate with patients' clinical and molecular characteristics in acute myeloid leukemia.Frontiers in immunology · 2023Article
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Authors and funding
18 authors at 5 institutions in 3 countries.
Funding
Abstract
The ability to identify and track T-cell receptor (TCR) sequences from patient samples is becoming central to the field of cancer research and immunotherapy. Tracking genetically engineered T cells expressing TCRs that target specific tumor antigens is important to determine the persistence of these cells and quantify tumor responses. The available high-throughput method to profile TCR repertoires is generally referred to as TCR sequencing (TCR-Seq). However, the available TCR-Seq data are limited compared with RNA sequencing (RNA-Seq). In this paper, we have benchmarked the ability of RNA-Seq-based methods to profile TCR repertoires by examining 19 bulk RNA-Seq samples across 4 cancer cohorts including both T-cell-rich and T-cell-poor tissue types. We have performed a comprehensive evaluation of the existing RNA-Seq-based repertoire profiling methods using targeted TCR-Seq as the gold standard. We also highlighted scenarios under which the RNA-Seq approach is suitable and can provide comparable accuracy to the TCR-Seq approach. Our results show that RNA-Seq-based methods are able to effectively capture the clonotypes and estimate the diversity of TCR repertoires, as well as provide relative frequencies of clonotypes in T-cell-rich tissues and low-diversity repertoires. However, RNA-Seq-based TCR profiling methods have limited power in T-cell-poor tissues, especially in highly diverse repertoires of T-cell-poor tissues. The results of our benchmarking provide an additional appealing argument to incorporate RNA-Seq into the immune repertoire screening of cancer patients as it offers broader knowledge into the transcriptomic changes that exceed the limited information provided by TCR-Seq.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.