ArticleJournal of immunology (Baltimore, Md. : 1950)2012
The inference of phased haplotypes for the immunoglobulin H chain V region gene loci by analysis of VDJ gene rearrangements.
Article in Journal of immunology (Baltimore, Md. : 1950), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed, 103 citations in OpenAlex.
- Characterization of immunoglobulin loci inNAR genomics and bioinformatics · 2026Article
- VDJ-Insights: simplifying the annotation of genomic immunoglobulin and T cell receptor regions.Bioinformatics (Oxford, England) · 2026Article
- Epigenetic-Genetic Coupling and Understanding the Molecular and Cellular Basis of Lamarckian Inheritance.International journal of molecular sciences · 2026Review
- The complex role of glycine N-methyltransferase in metabolism-a review.Molecular biology reports · 2025Review
- Addressing Technical Pitfalls in Pursuit of Molecular Factors That Mediate Immunoglobulin Gene Regulation.Journal of immunology (Baltimore, Md. : 1950) · 2024Article
- Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry.Genes and immunity · 2024Article
- IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data.Nucleic acids research · 2023Article
- Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire.Nature communications · 2023Article
- FLAIRR-Seq: A Method for Single-Molecule Resolution of Near Full-Length Antibody H Chain Repertoires.Journal of immunology (Baltimore, Md. : 1950) · 2023Article
- Frequent use of IGHV3-30-3 in SARS-CoV-2 neutralizing antibody responses.Frontiers in virology (Lausanne, Switzerland) · 2023Article
- Analysis of IGH allele content in a sample group of rheumatoid arthritis patients demonstrates unrevealed population heterogeneity.Frontiers in immunology · 2023Article
- Immunoglobulin genes, reproductive isolation and vertebrate speciation.Immunology and cell biology · 2022Article
- T cell receptor beta germline variability is revealed by inference from repertoire data.Genome medicine · 2022Article
- A BALB/c IGHV Reference Set, Defined by Haplotype Analysis of Long-Read VDJ-C Sequences From F1 (BALB/c x C57BL/6) Mice.Frontiers in immunology · 2022Article
- Addressing IGHV Gene Structural Diversity Enhances Immunoglobulin Repertoire Analysis: Lessons From Rhesus Macaque.Frontiers in immunology · 2022Article
- Igh Locus Polymorphism May Dictate Topological Chromatin Conformation and V Gene Usage in the Ig Repertoire.Frontiers in immunology · 2021Review
- Germline immunoglobulin genes: disease susceptibility genes hidden in plain sight?Current opinion in systems biology · 2020Article
- Inter- and intraspecies comparison of phylogenetic fingerprints and sequence diversity of immunoglobulin variable genes.Immunogenetics · 2020Article
- Polymorphisms in human immunoglobulin heavy chain variable genes and their upstream regions.Nucleic acids research · 2020Article
- Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species.PLoS computational biology · 2020Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
Abstract
The existence of many highly similar genes in the lymphocyte receptor gene loci makes them difficult to investigate, and the determination of phased "haplotypes" has been particularly problematic. However, V(D)J gene rearrangements provide an opportunity to infer the association of Ig genes along the chromosomes. The chromosomal distribution of H chain genes in an Ig genotype can be inferred through analysis of VDJ rearrangements in individuals who are heterozygous at points within the IGH locus. We analyzed VDJ rearrangements from 44 individuals for whom sufficient unique rearrangements were available to allow comprehensive genotyping. Nine individuals were identified who were heterozygous at the IGHJ6 locus and for whom sufficient suitable VDJ rearrangements were available to allow comprehensive haplotyping. Each of the 18 resulting IGHV│IGHD│IGHJ haplotypes was unique. Apparent deletion polymorphisms were seen that involved as many as four contiguous, functional IGHV genes. Two deletion polymorphisms involving multiple contiguous IGHD genes were also inferred. Three previously unidentified gene duplications were detected, where two sequences recognized as allelic variants of a single gene were both inferred to be on a single chromosome. Phased genomic data brings clarity to the study of the contribution of each gene to the available repertoire of rearranged VDJ genes. Analysis of rearrangement frequencies suggests that particular genes may have substantially different yet predictable propensities for rearrangement within different haplotypes. Together with data highlighting the extent of haplotypic variation within the population, this suggests that there may be substantial variability in the available Ab repertoires of different individuals.
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