ArticlePLoS computational biology2020
Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Extensive peripheral immunoglobulin repertoire analyses in people with multiple sclerosis reveal disease-specific signatures and distinct treatment effects of disease modifying drugs.Journal of neuroinflammation · 2026Article
- Comprehensive Mapping of Immune Nanobody Repertoires with NanoMAP.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
- Explore antibody repertoire in the era of AI.Acta biochimica et biophysica Sinica · 2025Article
- Systemic 4-1BB stimulation augments extrafollicular memory B cell formation and recall responses during Plasmodium infection.Cell reports · 2025Article
- De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies.Genome research · 2025Article
- Article
- Immunomolecular and reactivity landscapes of gut IgA subclasses in homeostasis and inflammatory bowel disease.The Journal of experimental medicine · 2024Article
- New generalized metric based on branch length distance to compare B cell lineage trees.Algorithms for molecular biology : AMB · 2024Article
- Article
- Computational detection of antigen-specific B cell receptors following immunization.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Combining mutation and recombination statistics to infer clonal families in antibody repertoires.eLife · 2024Article
- Article
- nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework.PLoS computational biology · 2024Article
- Evaluating methods for B-cell clonal family assignment.bioRxiv : the preprint server for biology · 2024Article
- Single-cell immune repertoire analysis.Nature methods · 2024Review
- Systematic evaluation of B-cell clonal family inference approaches.BMC immunology · 2024Article
- Applying phylogenetic methods for species delimitation to distinguish B-cell clonal families.Frontiers in immunology · 2024Article
- FLAIRR-Seq: A Method for Single-Molecule Resolution of Near Full-Length Antibody H Chain Repertoires.Journal of immunology (Baltimore, Md. : 1950) · 2023Article
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2 authors.
Funding
Abstract
Adaptive immune receptor repertoire sequencing (AIRR-Seq) offers the possibility of identifying and tracking B cell clonal expansions during adaptive immune responses. Members of a B cell clone are descended from a common ancestor and share the same initial V(D)J rearrangement, but their B cell receptor (BCR) sequence may differ due to the accumulation of somatic hypermutations (SHMs). Clonal relationships are learned from AIRR-seq data by analyzing the BCR sequence, with the most common methods focused on the highly diverse junction region. However, clonally related cells often share SHMs which have been accumulated during affinity maturation. Here, we investigate whether shared SHMs in the V and J segments of the BCR can be leveraged along with the junction sequence to improve the ability to identify clonally related sequences. We develop independent distance functions that capture junction similarity and shared mutations, and combine these in a spectral clustering framework to infer the BCR clonal relationships. Using both simulated and experimental data, we show that this model improves both the sensitivity and specificity for identifying B cell clones. Source code for this method is freely available in the SCOPer (Spectral Clustering for clOne Partitioning) R package (version 0.2 or newer) in the Immcantation framework: www.immcantation.org under the AGPLv3 license.
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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.