ArticleFrontiers in immunology2019
Identification of Subject-Specific Immunoglobulin Alleles From Expressed Repertoire Sequencing Data.
Article in Frontiers in immunology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Human primary antibody response to vaccination follows a partially sequential class-switching program with a checkpoint at IGHG2.Cell reports. Medicine · 2026Article
- Maternal vaccination timing shapes the composition and maturation of antibody clonotypes transferred to the newborn.bioRxiv : the preprint server for biology · 2026Article
- An integrated human immunoglobulin germline resource linking allele diversity to expressed repertoire structure.bioRxiv : the preprint server for biology · 2026Article
- The Adaptive Immune Receptor Repertoire Knowledge Commons: An invitation to the community.Cell systems · 2025Article
- Genotyping of selected germline adaptive immune system loci using short-read sequencing data.Genome research · 2025Article
- Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR.Genome research · 2024Article
- Full-length single-cell BCR sequencing paired with RNA sequencing reveals convergent responses to pneumococcal vaccination.Communications biology · 2024Article
- An unbiased comparison of immunoglobulin sequence aligners.Briefings in bioinformatics · 2024Article
- Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry.Genes and immunity · 2024Article
- AS03 adjuvant enhances the magnitude, persistence, and clonal breadth of memory B cell responses to a plant-based COVID-19 vaccine in humans.Science immunology · 2024Article
- Article
- IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data.Nucleic acids research · 2023Article
- FLAIRR-Seq: A Method for Single-Molecule Resolution of Near Full-Length Antibody H Chain Repertoires.Journal of immunology (Baltimore, Md. : 1950) · 2023Article
- Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation.Genes and immunity · 2023Article
- AIRR-C IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes.Frontiers in immunology · 2023Article
- ImmunoTyper-SR: A computational approach for genotyping immunoglobulin heavy chain variable genes using short-read data.Cell systems · 2022Article
- Immunoglobulin genes, reproductive isolation and vertebrate speciation.Immunology and cell biology · 2022Article
- Variations in antibody repertoires correlate with vaccine responses.Genome research · 2022Article
- T cell receptor beta germline variability is revealed by inference from repertoire data.Genome medicine · 2022Article
- Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation.Methods in molecular biology (Clifton, N.J.) · 2022Article
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9 authors.
Funding
Abstract
The adaptive immune receptor repertoire (AIRR) contains information on an individuals' immune past, present and potential in the form of the evolving sequences that encode the B cell receptor (BCR) repertoire. AIRR sequencing (AIRR-seq) studies rely on databases of known BCR germline variable (V), diversity (D), and joining (J) genes to detect somatic mutations in AIRR-seq data via comparison to the best-aligning database alleles. However, it has been shown that these databases are far from complete, leading to systematic misidentification of mutated positions in subsets of sample sequences. We previously presented TIgGER, a computational method to identify subject-specific V gene genotypes, including the presence of novel V gene alleles, directly from AIRR-seq data. However, the original algorithm was unable to detect alleles that differed by more than 5 single nucleotide polymorphisms (SNPs) from a database allele. Here we present and apply an improved version of the TIgGER algorithm which can detect alleles that differ by any number of SNPs from the nearest database allele, and can construct subject-specific genotypes with minimal prior information. TIgGER predictions are validated both computationally (using a leave-one-out strategy) and experimentally (using genomic sequencing), resulting in the addition of three new immunoglobulin heavy chain V (IGHV) gene alleles to the IMGT repertoire. Finally, we develop a Bayesian strategy to provide a confidence estimate associated with genotype calls. All together, these methods allow for much higher accuracy in germline allele assignment, an essential step in AIRR-seq studies.
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