ArticleImmunology2006
No evidence for the use of DIR, D-D fusions, chromosome 15 open reading frames or VH replacement in the peripheral repertoire was found on application of an improved algorithm, JointML, to 6329 human immunoglobulin H rearrangements.
Article in Immunology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Unveiling inverted D genes and D-D fusions in human antibody repertoires unlocks novel antibody diversity.Communications biology · 2025Article
- Antibody repertoire sequencing analysis.Acta biochimica et biophysica Sinica · 2022Review
- Antibody heavy chain CDR3 length-dependent usage of human IGHJ4 and IGHJ6 germline genes.Antibody therapeutics · 2021Article
- Landscape of Non-canonical Cysteines in Human VCell reports · 2020Article
- ASAP-SML: An antibody sequence analysis pipeline using statistical testing and machine learning.PLoS computational biology · 2020Article
- AID Overlapping and Polη Hotspots Are Key Features of Evolutionary Variation Within the Human Antibody Heavy Chain (IGHV) Genes.Frontiers in immunology · 2020Article
- Inferred Allelic Variants of Immunoglobulin Receptor Genes: A System for Their Evaluation, Documentation, and Naming.Frontiers in immunology · 2019Review
- Nucleotide Composition of Human Ig Nontemplated Regions Depends on Trimming of the Flanking Gene Segments, and Terminal Deoxynucleotidyl Transferase Favors Adding Cytosine, Not Guanosine, in Most VDJ Rearrangements.Journal of immunology (Baltimore, Md. : 1950) · 2018Article
- The Bayesian optimist's guide to adaptive immune receptor repertoire analysis.Immunological reviews · 2018Review
- On being the right size: antibody repertoire formation in the mouse and human.Immunogenetics · 2018Review
- Beyond Hot Spots: Biases in Antibody Somatic Hypermutation and Implications for Vaccine Design.Frontiers in immunology · 2018Review
- V(D)J Rearrangement Is Dispensable for Producing CDR-H3 Sequence Diversity in a Gene Converting Species.Frontiers in immunology · 2018Article
- Analyzing Immunoglobulin Repertoires.Frontiers in immunology · 2018Review
- Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation.Frontiers in immunology · 2017Article
- VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.BMC bioinformatics · 2016Article
- repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data.Bioinformatics (Oxford, England) · 2016Article
- Evidence of perturbed germinal center dynamics, but preserved antibody diversity, in end-stage renal disease.Immunity, inflammation and disease · 2016Article
- Immunoglobulin Classification Using the Colored Antibody Graph.Journal of computational biology : a journal of computational molecular cell biology · 2016Article
- BRILIA: Integrated Tool for High-Throughput Annotation and Lineage Tree Assembly of B-Cell Repertoires.Frontiers in immunology · 2016Article
- Assigning and visualizing germline genes in antibody repertoires.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2015Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Antibody diversity is created by imprecise joining of the variability (V), diversity (D) and joining (J) gene segments of the heavy and light chain loci. Analysis of rearrangements is complicated by somatic hypermutations and uncertainty concerning the sources of gene segments and the precise way in which they recombine. It has been suggested that D genes with irregular recombination signal sequences (DIR) and chromosome 15 open reading frames (OR15) can replace conventional D genes, that two D genes or inverted D genes may be used and that the repertoire can be further diversified by heavy chain V gene (VH) replacement. Safe conclusions require large, well-defined sequence samples and algorithms minimizing stochastic assignment of segments. Two computer programs were developed for analysis of heavy chain joints. JointHMM is a profile hidden Markow model, while JointML is a maximum-likelihood-based method taking the lengths of the joint and the mutational status of the VH gene into account. The programs were applied to a set of 6329 clonally unrelated rearrangements. A conventional D gene was found in 80% of unmutated sequences and 64% of mutated sequences, while D-gene assignment was kept below 5% in artificial (randomly permutated) rearrangements. No evidence for the use of DIR, OR15, multiple D genes or VH replacements was found, while inverted D genes were used in less than 1 per thousand of the sequences. JointML was shown to have a higher predictive performance for D-gene assignment in mutated and unmutated sequences than four other publicly available programs. An online version 1.0 of JointML is available at http://www.cbs.dtu.dk/services/VDJsolver.
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