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View article: Population-level genomic analysis of immunoglobulin loci variation in rhesus macaques reveals extensive germline diversity
Population-level genomic analysis of immunoglobulin loci variation in rhesus macaques reveals extensive germline diversity Open
Rhesus macaques (RMs) are a vital model for studying human disease and are invaluable to preclinical vaccine research, particularly for the study of broadly neutralizing antibody responses. Such studies require robust genetic resources for…
View article: The current landscape of adaptive immune receptor genomic and repertoire data: OGRDB and VDJbase
The current landscape of adaptive immune receptor genomic and repertoire data: OGRDB and VDJbase Open
Accurate characterization of adaptive immune receptor repertoires through high-throughput sequencing is critical for understanding immune responses, disease biomarkers, vaccine design, and antibody engineering. However, progress depends on…
View article: nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework 9075
nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework 9075 Open
Description Sequencing the Adaptive Immune Receptor Repertoire (AIRR) is a valuable experimental tool for probing the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Se…
View article: Adaptive immune receptor repertoire knowledge commons: large-scale knowledge for research and innovation (https://airr-knowledgeorg) 3765
Adaptive immune receptor repertoire knowledge commons: large-scale knowledge for research and innovation (https://airr-knowledgeorg) 3765 Open
Description The Adaptive Immune Receptor Repertoire Knowledge Commons (AKC) is a publicly accessible repository of data and knowledge about 1) adaptive immune receptors (AIRs) and AIR repertoires, 2) the complex genomic loci encoding AIR g…
View article: The human IG heavy chain constant gene locus is enriched for large structural variants and coding polymorphisms that vary among human populations
The human IG heavy chain constant gene locus is enriched for large structural variants and coding polymorphisms that vary among human populations Open
The human immunoglobulin heavy chain constant (IGHC) domain of antibodies (Abs) is responsible for effector functions critical to immunity. This domain is encoded by genes in the IGHC locus, where descriptions of genomic diversity remain i…
View article: The gremlin in the works: why T cell receptor researchers need to pay more attention to germline reference sequences
The gremlin in the works: why T cell receptor researchers need to pay more attention to germline reference sequences Open
The rise of T cell receptor (TCR) sequencing technologies is driving both new understandings of the immune system and the development of novel clinical platforms. Such analyses rely on comparing recombined TCR sequences to unrearranged ger…
View article: Building immunoglobulin and T cell receptor gene databases for the future
Building immunoglobulin and T cell receptor gene databases for the future Open
Genetic databases for immunoglobulin (IG) and T cell receptor (TR) genes have evolved from small catalogs to critical resources underpinning immunogenetic research. Accurate annotation enables the analysis of repertoire diversity, somatic …
View article: Germline polymorphisms in the immunoglobulin kappa and lambda loci explain variation in the expressed light chain antibody repertoire
Germline polymorphisms in the immunoglobulin kappa and lambda loci explain variation in the expressed light chain antibody repertoire Open
Variation in antibody (Ab) responses contributes to variable disease outcomes and therapeutic responsiveness, the determinants of which are incompletely understood. This study demonstrates that polymorphisms in immunoglobulin (IG) light ch…
View article: Enhancing sequence alignment of adaptive immune receptors through multi-task deep learning
Enhancing sequence alignment of adaptive immune receptors through multi-task deep learning Open
Sequence alignment of immunoglobulin (Ig) sequences is central to the computational analysis of adaptive immune receptor repertoire sequencing (AIRR-seq) data, impacting adaptive immunity research and antibody engineering. Traditional Ig s…
View article: Germline-encoded recognition of peanut underlies development of convergent antibodies in humans
Germline-encoded recognition of peanut underlies development of convergent antibodies in humans Open
Humans develop immunoglobulin G (IgG) antibodies to the foods they consume. In the context of food allergy, allergen-specific IgG antibodies can sequentially class-switch to pathogenic IgE. However, the mechanism underlying the antigenicit…
View article: Germline polymorphism in the immunoglobulin kappa and lambda loci explain variation in the expressed light chain antibody repertoire
Germline polymorphism in the immunoglobulin kappa and lambda loci explain variation in the expressed light chain antibody repertoire Open
Variation in antibody (Ab) responses contributes to variable disease outcomes and therapeutic responsiveness, the determinants of which are incompletely understood. This study demonstrates that polymorphisms in immunoglobulin (IG) light ch…
View article: The human IG heavy chain constant gene locus is enriched for large structural variants and coding polymorphisms that vary among human populations
The human IG heavy chain constant gene locus is enriched for large structural variants and coding polymorphisms that vary among human populations Open
The human immunoglobulin heavy chain constant (IGHC) domain of antibodies (Ab) is responsible for effector functions critical to immunity. This domain is encoded by genes in the IGHC locus, where descriptions of genomic diversity remain in…
View article: Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning
Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning Open
Machine learning (ML) has shown great potential in the adaptive immune receptor repertoire (AIRR) field. However, there is a lack of large-scale ground-truth experimental AIRR data suitable for AIRR-ML-based disease diagnostics and therape…
View article: A Broad Survey and Functional Analysis of Immunoglobulin Loci Variation in Rhesus Macaques
A Broad Survey and Functional Analysis of Immunoglobulin Loci Variation in Rhesus Macaques Open
Rhesus macaques (RMs) are a vital model for studying human disease and invaluable to pre-clinical vaccine research, particularly for the study of broadly neutralizing antibody responses. Such studies require robust genetic resources for an…
View article: An unbiased comparison of immunoglobulin sequence aligners
An unbiased comparison of immunoglobulin sequence aligners Open
Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is critical for our understanding of the adaptive immune system’s dynamics in health and disease. Reliable analysis of AIRR-seq data depends on accurate rearranged immunoglobulin (I…
View article: nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework
nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework Open
Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools hav…
View article: An unbiased comparison of immunoglobulin sequence aligners
An unbiased comparison of immunoglobulin sequence aligners Open
Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is critical for our under-standing of the adaptive immune system’s dynamics in health and disease. Reliable analysis of AIRR-seq data depends on accurate Immunoglobulin (Ig) sequenc…
View article: Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data
Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data Open
Enhancing the reproducibility and comprehension of adaptive immune receptor repertoire sequencing (AIRR-seq) data analysis is critical for scientific progress. This study presents guidelines for reproducible AIRR-seq data analysis, and a c…
View article: Digger: directed annotation of immunoglobulin and T cell receptor V, D, and J gene sequences and assemblies
Digger: directed annotation of immunoglobulin and T cell receptor V, D, and J gene sequences and assemblies Open
Summary Knowledge of immunoglobulin and T cell receptor encoding genes is derived from high-quality genomic sequencing. High-throughput sequencing is delivering large volumes of data, and precise, high-throughput approaches to annotation a…
View article: AIRR-C IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes
AIRR-C IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes Open
Introduction Analysis of an individual’s immunoglobulin (IG) gene repertoire requires the use of high-quality germline gene reference sets. When sets only contain alleles supported by strong evidence, AIRR sequencing (AIRR-seq) data analys…
View article: nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework
nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework Open
Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools hav…
View article: Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry
Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry Open
Immunoglobulins (IGs), critical components of the human immune system, are composed of heavy and light protein chains encoded at three genomic loci. The IG Kappa (IGK) chain locus consists of two large, inverted segmental duplications. The…
View article: Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning
Simulation of adaptive immune receptors and repertoires with complex immune information to guide the development and benchmarking of AIRR machine learning Open
Machine learning (ML) has shown great potential in the adaptive immune receptor repertoire (AIRR) field. However, there is a lack of large-scale ground-truth experimental AIRR data suitable for AIRR-ML-based disease diagnostics and therape…
View article: AIRR-C Human IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes
AIRR-C Human IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes Open
Analysis of an individual’s immunoglobulin (IG) gene repertoire requires the use of high-quality germline gene Reference Sets. The Adaptive Immune Receptor Repertoire-Community (AIRR-C) Reference Sets have been developed to include only hu…
View article: IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data
IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data Open
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…