ArticleImmunome research2010
Clustering-based identification of clonally-related immunoglobulin gene sequence sets.
Article in Immunome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 40 citations in OpenAlex.
- Alignment free identification of clones in B cell receptor repertoires.Nucleic acids research · 2021Article
- Evidence of Alternative Modes of B Cell Activation Involving Acquired Fab Regions of N-Glycosylation in Antibody-Secreting Cells Infiltrating the Labial Salivary Glands of Patients With Sjögren's Syndrome.Arthritis & rheumatology (Hoboken, N.J.) · 2018Article
- Optimized Threshold Inference for Partitioning of Clones From High-Throughput B Cell Repertoire Sequencing Data.Frontiers in immunology · 2018Article
- Deep sequencing of blood and gut T-cell receptor β-chains reveals gluten-induced immune signatures in celiac disease.Scientific reports · 2017Article
- Hierarchical Clustering Can Identify B Cell Clones with High Confidence in Ig Repertoire Sequencing Data.Journal of immunology (Baltimore, Md. : 1950) · 2017Article
- How B-Cell Receptor Repertoire Sequencing Can Be Enriched with Structural Antibody Data.Frontiers in immunology · 2017Review
- Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses.Frontiers in immunology · 2017Article
- Article
- Temporal stability and molecular persistence of the bone marrow plasma cell antibody repertoire.Nature communications · 2016Observational
- VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.BMC bioinformatics · 2016Article
- Likelihood-Based Inference of B Cell Clonal Families.PLoS computational biology · 2016Article
- Practical guidelines for B-cell receptor repertoire sequencing analysis.Genome medicine · 2015Review
- Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data.Bioinformatics (Oxford, England) · 2015Article
- Assigning and visualizing germline genes in antibody repertoires.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2015Article
- Utilities for High-Throughput Analysis of B-Cell Clonal Lineages.Journal of immunology research · 2015Article
- Characterizing immune repertoires by high throughput sequencing: strategies and applications.Trends in immunology · 2014Review
- pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires.Bioinformatics (Oxford, England) · 2014Article
- Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing.BMC genomics · 2014Article
- The promise and challenge of high-throughput sequencing of the antibody repertoire.Nature biotechnology · 2014Review
- IgE-associated IGHV genes from venom and peanut allergic individuals lack mutational evidence of antigen selection.PloS one · 2014Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundClonal expansion of B lymphocytes coupled with somatic mutation and antigen selection allow the mammalian humoral immune system to generate highly specific immunoglobulins (IG) or antibodies against invading bacteria, viruses and toxins. The availability of high-throughput DNA sequencing methods is providing new avenues for studying this clonal expansion and identifying the factors guiding the generation of antibodies. The identification of groups of rearranged immunoglobulin gene sequences descended from the same rearrangement (clonally-related sets) in very large sets of sequences is facilitated by the availability of immunoglobulin gene sequence alignment and partitioning software that can accurately predict component germline gene, but has required painstaking visual inspection and analysis of sequences.
resultsWe have developed and implemented an algorithm for identifying sets of clonally-related sequences in large human immunoglobulin heavy chain gene variable region sequence sets. The program processes sequences that have been partitioned using iHMMune-align, and uses pairwise comparisons of CDR3 sequences and similarity in IGHV and IGHJ germline gene assignments to construct a distance matrix. Agglomerative hierarchical clustering is then used to identify likely groups of clonally-related sequences. The program is available for download from http://www.cse.unsw.edu.au/~ihmmune/ClonalRelate/ClonalRelate.zip.
conclusionsThe method was evaluated on several benchmark datasets and provided a more accurate and considerably faster identification of clonally-related immunoglobulin gene sequences than visual inspection by domain experts.
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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.