ArticleNucleic acids research2023
IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 19 citations in OpenAlex.
- An integrated human immunoglobulin germline resource linking allele diversity to expressed repertoire structure.bioRxiv : the preprint server for biology · 2026Article
- Population-level genomic analysis of immunoglobulin loci variation in rhesus macaques reveals extensive germline diversity.Immunity · 2026Article
- The current landscape of adaptive immune receptor genomic and repertoire data: OGRDB and VDJbase.Nucleic acids research · 2026Article
- Is the vaccination-induced B cell receptor repertoire predictable?Immunoinformatics (Amsterdam, Netherlands) · 2025Article
- Enhancing sequence alignment of adaptive immune receptors through multi-task deep learning.Nucleic acids research · 2025Article
- De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies.Genome research · 2025Article
- Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning.Nucleic acids research · 2025Article
- Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR.Genome research · 2024Article
- An unbiased comparison of immunoglobulin sequence aligners.Briefings in bioinformatics · 2024Article
- 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
- Biophysical cartography of the native and human-engineered antibody landscapes quantifies the plasticity of antibody developability.Communications biology · 2024Article
- Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data.Briefings in bioinformatics · 2024Article
- Human immunoglobulin gene allelic variation impacts germline-targeting vaccine priming.NPJ vaccines · 2024Article
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Authors and funding
12 authors at 7 institutions in 5 countries.
Funding
Abstract
In adaptive immune receptor repertoire analysis, determining the germline variable (V) allele associated with each T- and B-cell receptor sequence is a crucial step. This process is highly impacted by allele annotations. Aligning sequences, assigning them to specific germline alleles, and inferring individual genotypes are challenging when the repertoire is highly mutated, or sequence reads do not cover the whole V region. Here, we propose an alternative naming scheme for the V alleles, as well as a novel method to infer individual genotypes. We demonstrate the strengths of the two by comparing their outcomes to other genotype inference methods. We validate the genotype approach with independent genomic long-read data. The naming scheme is compatible with current annotation tools and pipelines. Analysis results can be converted from the proposed naming scheme to the nomenclature determined by the International Union of Immunological Societies (IUIS). Both the naming scheme and the genotype procedure are implemented in a freely available R package (PIgLET https://bitbucket.org/yaarilab/piglet). To allow researchers to further explore the approach on real data and to adapt it for their uses, we also created an interactive website (https://yaarilab.github.io/IGHV_reference_book).
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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.