scholarly journals Knowledge-based antibody repertoire simulation, a novel allele detection tool evaluation and application

2021 ◽  
Author(s):  
Xiujia Yang ◽  
Yan Zhu ◽  
Huikun Zeng ◽  
Sen Chen ◽  
Junjie Guan ◽  
...  
Keyword(s):  
Humoral Immunity ◽  
Antibody Repertoire ◽  
Detailed Knowledge ◽  
Allele Detection ◽  
Full Spectrum ◽  
Knowledge Based ◽  
Gene Usage ◽  
Repertoire Sequencing ◽  
Novel Alleles ◽  
Novel Allele

Detailed knowledge of the diverse immunoglobulin germline genes is critical for the study of humoral immunity. Hundreds of alleles have been discovered by analyzing antibody repertoire sequencing (Rep-seq or Ig-seq) data via multiple novel allele detection tools (NADTs). However, the performance of these NADTs through antibody sequences with intrinsic somatic hypermutations (SHMs) is unclear. Here, we developed a tool to simulate repertoires by integrating the full spectrum features of an antibody repertoire such as germline gene usage, junctional modification, position-specific SHM and clonal expansion based on 2152 high-quality datasets. We then systematically evaluated these NADTs using both simulated and genuine Ig-seq datasets. Finally, we applied these NADTs to 687 Ig-seq datasets and identified 43 novel alleles using defined criteria. Twenty-five alleles were validated through findings of other sources. In addition to the novel alleles detected, our simulation tool, the results of our comparison, and the streamline of this process may benefit further humoral immunity studies via Ig-seq.

scholarly journals Novel Allele Detection Tool Benchmark and Application With Antibody Repertoire Sequencing Dataset

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiujia Yang ◽  
Yan Zhu ◽  
Sen Chen ◽  
Huikun Zeng ◽  
Junjie Guan ◽  
...  
Keyword(s):  
Humoral Immunity ◽  
Antibody Repertoire ◽  
Detailed Knowledge ◽  
Allele Detection ◽  
Full Spectrum ◽  
Detection Tool ◽  
Germline Genes ◽  
Gene Usage ◽  
Repertoire Sequencing ◽  
Novel Allele

Detailed knowledge of the diverse immunoglobulin germline genes is critical for the study of humoral immunity. Hundreds of alleles have been discovered by analyzing antibody repertoire sequencing (Rep-seq or Ig-seq) data via multiple novel allele detection tools (NADTs). However, the performance of these NADTs through antibody sequences with intrinsic somatic hypermutations (SHMs) is unclear. Here, we developed a tool to simulate repertoires by integrating the full spectrum features of an antibody repertoire such as germline gene usage, junctional modification, position-specific SHM and clonal expansion based on 2152 high-quality datasets. We then systematically evaluated these NADTs using both simulated and genuine Ig-seq datasets. Finally, we applied these NADTs to 687 Ig-seq datasets and identified 43 novel allele candidates (NACs) using defined criteria. Twenty-five alleles were validated through findings of other sources. In addition to the NACs detected, our simulation tool, the results of our comparison, and the streamline of this process may benefit further humoral immunity studies via Ig-seq.

scholarly journals Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles

2015 ◽  
Vol 112 (8) ◽  
pp. E862-E870 ◽  
Author(s):  
Daniel Gadala-Maria ◽  
Gur Yaari ◽  
Mohamed Uduman ◽  
Steven H. Kleinstein
Keyword(s):  
B Cell ◽  
Large Scale ◽  
Gene Segment ◽  
Automated Analysis ◽  
Sequencing Data ◽  
Cell Repertoire ◽  
Accurate Analysis ◽  
V Genes ◽  
Repertoire Sequencing ◽  
Novel Alleles

Individual variation in germline and expressed B-cell immunoglobulin (Ig) repertoires has been associated with aging, disease susceptibility, and differential response to infection and vaccination. Repertoire properties can now be studied at large-scale through next-generation sequencing of rearranged Ig genes. Accurate analysis of these repertoire-sequencing (Rep-Seq) data requires identifying the germline variable (V), diversity (D), and joining (J) gene segments used by each Ig sequence. Current V(D)J assignment methods work by aligning sequences to a database of known germline V(D)J segment alleles. However, existing databases are likely to be incomplete and novel polymorphisms are hard to differentiate from the frequent occurrence of somatic hypermutations in Ig sequences. Here we develop a Tool for Ig Genotype Elucidation via Rep-Seq (TIgGER). TIgGER analyzes mutation patterns in Rep-Seq data to identify novel V segment alleles, and also constructs a personalized germline database containing the specific set of alleles carried by a subject. This information is then used to improve the initial V segment assignments from existing tools, like IMGT/HighV-QUEST. The application of TIgGER to Rep-Seq data from seven subjects identified 11 novel V segment alleles, including at least one in every subject examined. These novel alleles constituted 13% of the total number of unique alleles in these subjects, and impacted 3% of V(D)J segment assignments. These results reinforce the highly polymorphic nature of human Ig V genes, and suggest that many novel alleles remain to be discovered. The integration of TIgGER into Rep-Seq processing pipelines will increase the accuracy of V segment assignments, thus improving B-cell repertoire analyses.

scholarly journals Accurate Immune Repertoire Sequencing Reveals Malaria Infection Driven Antibody Lineage Diversification in Young Children

2017 ◽  
Author(s):  
Ben S. Wendel ◽  
Chenfeng He ◽  
Mingjuan Qu ◽  
Di Wu ◽  
Stefany M. Hernandez ◽  
...  
Keyword(s):  
B Cells ◽  
Somatic Hypermutation ◽  
Antibody Repertoire ◽  
Infants And Toddlers ◽  
High Coverage ◽  
Sequence Composition ◽  
Age Related ◽  
Sequencing Method ◽  
Repertoire Sequencing ◽  
Lineage Diversification

ABSTRACTAccurately measuring antibody repertoire sequence composition in a small amount of blood is challenging yet important to the understanding of the repertoire response to infections and vaccinations. Here, we describe an accurate and high-coverage repertoire sequencing method, MIDCIRS, which uses as few as 1,000 naïve B cells. Using it, we studied age-related antibody repertoire development and diversification before and during acute malaria in infants (< 12 months old) and toddlers (12 – 47 months old) with 4-8 ml of blood draws. Unexpectedly, we discovered high levels of somatic hypermutation (SHM) in infants as young as three months old. Antibody clonal lineage analysis revealed that both infants and toddlers increase SHM levels upon infection and memory B cells isolated from pre-malaria samples in malaria-experienced individuals continue to induce SHMs upon malaria rechallenge. These results highlight the vast potential of antibody repertoire diversification in infants and toddlers that has not been realized previously.

scholarly journals Dual UMIs and Dual Barcodes With Minimal PCR Amplification Removes Artifacts and Acquires Accurate Antibody Repertoire

2021 ◽  
Vol 12 ◽  
Author(s):  
Qilong Wang ◽  
Huikun Zeng ◽  
Yan Zhu ◽  
Minhui Wang ◽  
Yanfang Zhang ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Antibody Repertoire ◽  
Consensus Building ◽  
Chain Reaction ◽  
Single Nucleotide ◽  
False Discovery ◽  
Novel Approach ◽  
Repertoire Sequencing ◽  
Polymerase Chain ◽  
Antibody Repertoires

Antibody repertoire sequencing (Rep-seq) has been widely used to reveal repertoire dynamics and to interrogate antibodies of interest at single nucleotide-level resolution. However, polymerase chain reaction (PCR) amplification introduces extensive artifacts including chimeras and nucleotide errors, leading to false discovery of antibodies and incorrect assessment of somatic hypermutations (SHMs) which subsequently mislead downstream investigations. Here, a novel approach named DUMPArts, which improves the accuracy of antibody repertoires by labeling each sample with dual barcodes and each molecule with dual unique molecular identifiers (UMIs) via minimal PCR amplification to remove artifacts, is developed. Tested by ultra-deep Rep-seq data, DUMPArts removed inter-sample chimeras, which cause artifactual shared clones and constitute approximately 15% of reads in the library, as well as intra-sample chimeras with erroneous SHMs and constituting approximately 20% of the reads, and corrected base errors and amplification biases by consensus building. The removal of these artifacts will provide an accurate assessment of antibody repertoires and benefit related studies, especially mAb discovery and antibody-guided vaccine design.

scholarly journals Multi-Donor Longitudinal Antibody Repertoire Sequencing Reveals the Existence of Public Antibody Clonotypes in HIV-1 Infection

2018 ◽  
Vol 23 (6) ◽  
pp. 845-854.e6 ◽  
Author(s):  
Ian Setliff ◽  
Wyatt J. McDonnell ◽  
Nagarajan Raju ◽  
Robin G. Bombardi ◽  
Amyn A. Murji ◽  
...  
Keyword(s):  
Antibody Repertoire ◽  
Repertoire Sequencing ◽  
Hiv 1

scholarly journals Simple paired heavy- and light-chain antibody repertoire sequencing using endoplasmic reticulum microsomes

2018 ◽  
Vol 10 (1) ◽  
Author(s):  
Praneeth Reddy Devulapally ◽  
Jörg Bürger ◽  
Thorsten Mielke ◽  
Zoltán Konthur ◽  
Hans Lehrach ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Light Chain ◽  
Antibody Repertoire ◽  
Repertoire Sequencing ◽  
Light Chain Antibody

Knowledge Based Qualification Methodology to Evaluate Shock Induced Risks in BGA Components

2017 ◽  
Author(s):  
Min Pei ◽  
Guru Arakere ◽  
Milena Vujosevic
Keyword(s):  
User Behavior ◽  
System Level ◽  
Special Focus ◽  
Detailed Knowledge ◽  
End User ◽  
Physics Of Failure ◽  
Knowledge Based ◽  
Test Board ◽  
Deformation Modes

This paper provides details of Knowledge Based Qualification (KBQ) methodology to calculate BGA component shock qualification requirements. The methodology is based on experimental, theoretical and computational approach used to generate a detailed knowledge of the use conditions and failure physics. Discussed are the steps taken to understand the end-user behavior and system design impact on dynamic load experienced by the component in the field. A special focus is placed on the understanding of the board deformation modes, their impact on BGA failures, and the physics-of-failure (PoF) metric that is not only accurate enough but also practical for everyday applications. Theoretical and computational modeling was used to perform the necessary “translations” from use condition to test conditions and from system level drop to test board component shock. These “translations” enabled by the PoF metric, directly lead to the determination of BGA shock qualification requirements.

scholarly journals Public Immunity: Evolutionary Spandrels for Pathway-Amplifying Protective Antibodies

2021 ◽  
Vol 12 ◽  
Author(s):  
Maya Sangesland ◽  
Daniel Lingwood
Keyword(s):  
B Cell ◽  
Humoral Immunity ◽  
Cell Receptor ◽  
B Cell Receptor ◽  
Antibody Responses ◽  
Antibody Repertoire ◽  
Protective Antibodies ◽  
Cognate Antigen ◽  
Rational Vaccine Design ◽  
Antigen Reactivity

Humoral immunity is seeded by affinity between the B cell receptor (BCR) and cognate antigen. While the BCR is a chimeric display of diverse antigen engagement solutions, we discuss its functional activity as an ‘innate-like’ immune receptor, wherein genetically hardwired antigen complementarity can serve as reproducible templates for pathway-amplifying otherwise immunologically recessive antibody responses. We propose that the capacity for germline reactivity to new antigen emerged as a set of evolutionary spandrels or coupled traits, which can now be exploited by rational vaccine design to focus humoral immunity upon conventionally immune-subdominant antibody targets. Accordingly, we suggest that evolutionary spandrels account for the necessary but unanticipated antigen reactivity of the germline antibody repertoire.

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