ArticleBMC immunology2014
Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice.
Article in BMC immunology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
42 citing papers in PubMed.
- SatTCR: a pipeline for performing saturation analysis of the T cell receptor repertoire and a case study of a healthy canine.MethodsX · 2026Article
- From Single Cells to Silicon: Emerging Technologies Transforming Monoclonal Antibody Discovery.Antibodies (Basel, Switzerland) · 2026Review
- Identification of a type 1 diabetes-associated T cell receptor repertoire signature from the human peripheral blood.Science advances · 2026Article
- Review
- Profiling T Cell Receptor and Immunoglobulin Repertoires Through RNA Sequencing to Understand Host Response to Trypanosoma cruzi Infection.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Machine learning for precision diagnostics of autoimmunity.Scientific reports · 2024Article
- Enhancing comparative T cell receptor repertoire analysis in small biological samples through pooling homologous cell samples from multiple mice.Cell reports methods · 2024Article
- Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data.Briefings in bioinformatics · 2024Article
- Application and challenges of TCR and BCR sequencing to investigate T- and B-cell clonality in elastase-induced experimental murine abdominal aortic aneurysm.Frontiers in cardiovascular medicine · 2023Article
- Characterization of B cell receptor H-CDR3 repertoire of spleen in PRV-infected mice.BMC veterinary research · 2022Article
- TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences.Briefings in bioinformatics · 2022Article
- Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis.Methods in molecular biology (Clifton, N.J.) · 2022Article
- An Analysis of the Effects of Spaceflight and Vaccination on Antibody Repertoire Diversity.ImmunoHorizons · 2021Article
- A single donor is sufficient to produce a highly functional in vitro antibody library.Communications biology · 2021Article
- PASA: Proteomic analysis of serum antibodies web server.PLoS computational biology · 2021Article
- Antibody Repertoire Analysis of Tumor-Infiltrating B Cells Reveals Distinct Signatures and Distributions Across Tissues.Frontiers in immunology · 2021Article
- Article
- Uncoupling of invasive bacterial mucosal immunogenicity from pathogenicity.Nature communications · 2020Article
- Molecular T-Cell Repertoire Analysis as Source of Prognostic and Predictive Biomarkers for Checkpoint Blockade Immunotherapy.International journal of molecular sciences · 2020Review
- Recapitulation of posttransfusion purpura by cross-strain platelet immunization in mice.Blood advances · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext-generation sequencing (NGS) of antibody variable regions has emerged as a powerful tool in systems immunology by providing quantitative molecular information on polyclonal humoral immune responses. Reproducible and robust information on antibody repertoires is valuable for basic and applied immunology studies: thus, it is essential to establish the reliability of antibody NGS data.
resultsWe isolated RNA from antibody-secreting cells (ASCs) from either 1 mouse or a pool of 9 immunized mice in order to simulate both normal and high diversity populations. Next, we prepared three technical replicates of antibody libraries by RT-PCR from each diversity scenario, which were sequenced using the Illumina MiSeq platform resulting in >106 250 bp paired-end reads per replicate. We then assessed the robustness of antibody repertoire data based on clonal identification defined by amino acid sequence of either full-length VDJ region or the complementarity determining region 3 (CDR3). Leveraging modeling approaches adapted from mathematical ecology, we found that in either diversity scenario both CDR3 and VDJ detection nears completeness indicating deep coverage of ASC repertoires. Additionally, we defined reliability thresholds for accurate quantification and ranking of CDR3s and VDJs. Importantly, we show that both factors-(i) replicate sequencing and (ii) sequencing depth-are crucial for robust CDR3 and VDJ detection and ranking.
conclusionsIn summary, we established widely applicable experimental and computational guidelines for robust antibody NGS and analysis, which will help advance systems immunology studies related to the quantitative profiling of antibody responses following infection and vaccination.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.