ArticleJournal of immunology (Baltimore, Md. : 1950)2017
Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data.
Article in Journal of immunology (Baltimore, Md. : 1950), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers, 1 of them a synthesis that pooled it.
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Who cites it
114 citing papers in PubMed, 1 synthesis or guideline pooled it, 178 citations in OpenAlex.
- Anchor Clustering for million-scale immune repertoire sequencing data.BMC bioinformatics · 2024Pooled it
- Precise targeting of HIV broadly neutralizing antibody precursors in humans.Science (New York, N.Y.) · 2025Trial
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- Age-associated differences in XBB.1.5 trivalent booster vaccine-induced adaptive responses revealed by single-cell RNA sequencing.Emerging microbes & infections · 2026Article
- Transcriptomic characterization of transitional B cells reveals four subsets with perturbed activation profiles in scleroderma.iScience · 2026Article
- Article
- mRNA-based influenza vaccine expands the B cell response breadth in humans.Nature immunology · 2026Observational
- Central nervous system B cell multiomics reveals a legacy of immune dysregulation in long-term treated HIV infection.Science advances · 2026Article
- Primary sclerosing cholangitis displays distinct colonic mucosa topography yet a shared mast cell state with ulcerative colitis.Nature communications · 2026Article
- Granzyme B-expressing regulatory B cells share the same origin as conventional blood B cells.Biochemistry and biophysics reports · 2026Article
- SARS-CoV-2 infection and vaccination elicit distinct pharyngeal mucosal B cell responses in children.Nature communications · 2026Article
- Epitope-focused discovery of SARS-CoV-2 antibodies that potently neutralize Omicron variants.Nature microbiology · 2026Article
- Large-scale paired chain BCR analysis reveals antibody clonal family inference bias and enhances resolution with machine learning.PLoS computational biology · 2026Article
- EBV reprograms autoreactive anti-CNS B cells as antigen presenting cells in multiple sclerosis.bioRxiv : the preprint server for biology · 2026Article
- Profiling Allogeneic HLA-specific B-cell Responses Utilizing a 64-plex Single-HLA Reporter Cell Panel.bioRxiv : the preprint server for biology · 2026Article
- Functional Convergence of Genetically Diverse B-Cell Receptors in Simian-HIV Infected Rhesus Macaques.bioRxiv : the preprint server for biology · 2026Article
- DIS3 licenses B cells for plasma cell differentiation in humans.Cellular & molecular immunology · 2026Article
- Article
- Epstein-Barr virus reprograms autoreactive B cells as antigen-presenting cells in systemic lupus erythematosus.Science translational medicine · 2025Article
- Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus.Genome research · 2025Article
54 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Adaptive immunity is driven by the expansion, somatic hypermutation, and selection of B cell clones. Each clone is the progeny of a single B cell responding to Ag, with diversified Ig receptors. These receptors can now be profiled on a large scale by next-generation sequencing. Such data provide a window into the microevolutionary dynamics that drive successful immune responses and the dysregulation that occurs with aging or disease. Clonal relationships are not directly measured, but they must be computationally inferred from these sequencing data. Although several hierarchical clustering-based methods have been proposed, they vary in distance and linkage methods and have not yet been rigorously compared. In this study, we use a combination of human experimental and simulated data to characterize the performance of hierarchical clustering-based methods for partitioning sequences into clones. We find that single linkage clustering has high performance, with specificity, sensitivity, and positive predictive value all >99%, whereas other linkages result in a significant loss of sensitivity. Surprisingly, distance metrics that incorporate the biases of somatic hypermutation do not outperform simple Hamming distance. Although errors were more likely in sequences with short junctions, using the entire dataset to choose a single distance threshold for clustering is near optimal. Our results suggest that hierarchical clustering using single linkage with Hamming distance identifies clones with high confidence and provides a fully automated method for clonal grouping. The performance estimates we develop provide important context to interpret clonal analysis of repertoire sequencing data and allow for rigorous testing of other clonal grouping algorithms.
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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.