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 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 Comparison between Hybridoma and Fab/phage Anti-RhD: Their V Gene Usage and Pairings

2000 ◽  
Vol 16 (1-2) ◽  
pp. 15-19 ◽  
Author(s):  
W. S. Perera ◽  
M. T. Moss ◽  
S. J. Urbaniak
Keyword(s):  
Germline Gene ◽  
Germline Genes ◽  
Two Systems ◽  
Gene Usage ◽  
Hybridoma Technology ◽  
V Gene ◽  
Unique Genes

Our 11 anti-RhD's in conjunction with 37 previously published RhD antibodies, produced by hybridoma technology were analysed for germline gene usage and restriction in VHand VLpairings. The 17 VHgermline genes used by the hybridoma anti-RhD IgG were derived from 4 VH families (VH1, VH2, VH3 and VH4). Eighteen kappa chains were restricted to only 5 germline genes from only 2 Vκ families (Vκ1 and κ3). However, the 13 lambda chains were not as restricted, using 10 Vλgermline genes from 4 families (Vλ1, Vλ2, Vλ3 and Vλ8). Fifty six unique Fab/phage anti-RhD were also analysed. In all cases the Fab/phage VHgermline genes were derived from the VH3 family (41/41). The 29 kappa chains were restricted to 4 germline genes primarily from Vκ1 (97%) germline genes from 5 families (Vλ1, Vλ2, Vλ3, Vλ4 and Vλ7). The VHgermline genes of the Fab/phage were restricted to 4 of the 17 used by the hybridoma anti-RhD IgG (DP46, DP49, DP50 and DP77). Ninety percent of the Fab/phage were restricted to 1 of the 5 Vκgermline genes used by the IgG (DPK9). However, the repertoire of the Vλgermline genes used in these two systems is different, with analysis showing greater diversity in Vλgene usage with 8 unique germline genes used by 76% Fab/phage compared to 4 unique genes used by 46% hybriboma anti-RhD.

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

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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