Polymorphisms in human immunoglobulin heavy chain variable genes and their upstream regions
Germline variations in immunoglobulin genes influence the repertoire of B cell receptors and antibodies, and such polymorphisms may impact disease susceptibility. However, the knowledge of the genomic variation of the immunoglobulin loci is scarce. Here, we report 25 potential novel germline IGHV alleles as inferred from rearranged naïve B cell cDNA repertoires of 98 individuals.
VDJbase: an adaptive immune receptor genotype and haplotype database
VDJbase is a publicly available database that offers easy searching of data describing the complete sets of gene sequences (genotypes and haplotypes) inferred from adaptive immune receptor repertoire sequencing datasets. VDJbase is designed to act as a resource that will allow the scientific community to explore the genetic variability of the immunoglobulin (Ig) and T cell receptor (TR) gene loci.
RAbHIT: R Antibody Haplotype Inference Tool
RAbHIT is an R Haplotype Antibody Inference Tool, that implements a novel algorithm to infer V(D)J haplotypes by adapting a Bayesian framework. RAbHIT offers inference of haplotype and gene deletions. It may be applied to sequences from naïve and non-naïve B-cells, sequenced by different library preparation protocols.
immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking
immuneSIM enables in silico generation of single and paired chain human and mouse B- and T-cell repertoires with user-defined tunable properties to provide the user with experimental-like (or aberrant) data to benchmark their repertoire analysis methods.
High frequency of shared clonotypes in human B cell receptor repertoires
The human genome contains approximately 20 thousand protein-coding genes1, but the size of the collection of antigen receptors of the adaptive immune system that is generated by the recombination of gene segments with non-templated junctional additions (on B cells) is unknown—although it is certainly orders of magnitude larger.
HereReproducibility and Reuse of Adaptive Immune Receptor Repertoire Data
High-throughput sequencing (HTS) of immunoglobulin (B-cell receptor, antibody) and T-cell receptor repertoires has increased dramatically since the technique was introduced in 2009 (1–3). This experimental approach explores the maturation of the adaptive immune system and its response to antigens, pathogens, and disease conditions in exquisite detail.
Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data
Antigen specificity is a cardinal feature of adaptive immunity that underlies immune homeostasis and control of pathogenic attack in higher vertebrates.
Mosaic deletion patterns of the human antibody heavy chain gene locus shown by Bayesian haplotyping
Analysis of antibody repertoires by high-throughput sequencing is of major importance in understanding adaptive immune responses. Our knowledge of variations in the genomic loci encoding immunoglobulin genes is incomplete, resulting in conflicting VDJ gene assignments and biased genotype and haplotype inference.