ArticleNature biotechnology2021
Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases.
Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers, 1 of them a synthesis that pooled it.
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Who cites it
83 citing papers in PubMed, 1 synthesis or guideline pooled it.
- T-cell receptor variable region usage in Chagas disease: A systematic review of experimental and human studies.PLoS neglected tropical diseases · 2022Pooled it
- Nivolumab plus ipilimumab in advanced salivary gland cancer: a phase 2 trial.Nature medicine · 2023Trial
- Article
- T cell immunomonitoring: a comparative analysis of traditional and novel methods to quantify and characterize human antigen-specific T cells.Nature protocols · 2026Review
- T Cell Thoughts.Immunological reviews · 2026Review
- Thymic selection of the T cell receptor repertoire is biased toward autoimmunity in females.eLife · 2026Article
- Protocol for high-throughput genome-wide translocation sequencing-based profiling of T-cell receptor α and β gene rearrangements in mouse T cells.STAR protocols · 2026Article
- Machine Learning for TCR Repertoire Epitope Annotation and Pattern Discovery.Immunological reviews · 2026Review
- SatTCR: a pipeline for performing saturation analysis of the T cell receptor repertoire and a case study of a healthy canine.MethodsX · 2026Article
- Advances in predicting T cell epitope recognition for cancer immunotherapy.Nature cancer · 2026Review
- Decoding adaptive immunity: advanced strategies in T and B cell repertoire analysis.Journal of translational medicine · 2026Review
- Inference of SARS-CoV-2 exposure biomarkers using large-scale T-cell repertoire profiling.Genome medicine · 2026Article
- T cell receptor clonotypes predict human leukocyte antigen allele carriage and antigen exposure history.Communications biology · 2026Article
- NeoTCRseek: an integrated platform for high-sensitivity identification of neoantigen-specific TCR clonotypes to track clinical T-cell dynamics.Frontiers in immunology · 2026Article
- HTGTS-TCR-Seq for Profiling of Mouse and Human T-Cell Receptor α and β Gene Rearrangements and Diversity.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Plate-based 10X Genomics-compatible single-cell RNA-sequencing based on Smart-seq3xpress.BMC genomics · 2025Article
- Benchmarking unsupervised methods for inferring TCR specificity.NAR genomics and bioinformatics · 2025Review
- Harnessing TCR repertoires: predictive insights and therapeutic monitoring in cancer immunotherapy.Immuno-oncology technology · 2025Review
- Detection of Human Brain Cancers using Genomic and Immune Cell Characterization of Cerebrospinal Fluid through CSF-BAM.Cancer discovery · 2025Article
- T-cell Receptor Profiling of Blood to Detect Lung Cancer.Cancer immunology research · 2025Article
23 more citing papers are in PubMed but not listed here.
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Authors and funding
18 authors.
Funding
Abstract
Monitoring the T cell receptor (TCR) repertoire in health and disease can provide key insights into adaptive immune responses, but the accuracy of current TCR sequencing (TCRseq) methods is unclear. In this study, we systematically compared the results of nine commercial and academic TCRseq methods, including six rapid amplification of complementary DNA ends (RACE)-polymerase chain reaction (PCR) and three multiplex-PCR approaches, when applied to the same T cell sample. We found marked differences in accuracy and intra- and inter-method reproducibility for T cell receptor α (TRA) and T cell receptor β (TRB) TCR chains. Most methods showed a lower ability to capture TRA than TRB diversity. Low RNA input generated non-representative repertoires. Results from the 5' RACE-PCR methods were consistent among themselves but differed from the RNA-based multiplex-PCR results. Using an in silico meta-repertoire generated from 108 replicates, we found that one genomic DNA-based method and two non-unique molecular identifier (UMI) RNA-based methods were more sensitive than UMI methods in detecting rare clonotypes, despite the better clonotype quantification accuracy of the latter.
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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.