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

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,...

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Autores principales: Wang, Qilong, Zeng, Huikun, Zhu, Yan, Wang, Minhui, Zhang, Yanfang, Yang, Xiujia, Tang, Haipei, Li, Hongliang, Chen, Yuan, Ma, Cuiyu, Lan, Chunhong, Liu, Bin, Yang, Wei, Yu, Xueqing, Zhang, Zhenhai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8727365/
https://www.ncbi.nlm.nih.gov/pubmed/35003093
http://dx.doi.org/10.3389/fimmu.2021.778298
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author Wang, Qilong
Zeng, Huikun
Zhu, Yan
Wang, Minhui
Zhang, Yanfang
Yang, Xiujia
Tang, Haipei
Li, Hongliang
Chen, Yuan
Ma, Cuiyu
Lan, Chunhong
Liu, Bin
Yang, Wei
Yu, Xueqing
Zhang, Zhenhai
author_facet Wang, Qilong
Zeng, Huikun
Zhu, Yan
Wang, Minhui
Zhang, Yanfang
Yang, Xiujia
Tang, Haipei
Li, Hongliang
Chen, Yuan
Ma, Cuiyu
Lan, Chunhong
Liu, Bin
Yang, Wei
Yu, Xueqing
Zhang, Zhenhai
author_sort Wang, Qilong
collection PubMed
description 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.
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spelling pubmed-87273652022-01-06 Dual UMIs and Dual Barcodes With Minimal PCR Amplification Removes Artifacts and Acquires Accurate Antibody Repertoire Wang, Qilong Zeng, Huikun Zhu, Yan Wang, Minhui Zhang, Yanfang Yang, Xiujia Tang, Haipei Li, Hongliang Chen, Yuan Ma, Cuiyu Lan, Chunhong Liu, Bin Yang, Wei Yu, Xueqing Zhang, Zhenhai Front Immunol Immunology 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. Frontiers Media S.A. 2021-12-22 /pmc/articles/PMC8727365/ /pubmed/35003093 http://dx.doi.org/10.3389/fimmu.2021.778298 Text en Copyright © 2021 Wang, Zeng, Zhu, Wang, Zhang, Yang, Tang, Li, Chen, Ma, Lan, Liu, Yang, Yu and Zhang https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Immunology
Wang, Qilong
Zeng, Huikun
Zhu, Yan
Wang, Minhui
Zhang, Yanfang
Yang, Xiujia
Tang, Haipei
Li, Hongliang
Chen, Yuan
Ma, Cuiyu
Lan, Chunhong
Liu, Bin
Yang, Wei
Yu, Xueqing
Zhang, Zhenhai
Dual UMIs and Dual Barcodes With Minimal PCR Amplification Removes Artifacts and Acquires Accurate Antibody Repertoire
title Dual UMIs and Dual Barcodes With Minimal PCR Amplification Removes Artifacts and Acquires Accurate Antibody Repertoire
title_full Dual UMIs and Dual Barcodes With Minimal PCR Amplification Removes Artifacts and Acquires Accurate Antibody Repertoire
title_fullStr Dual UMIs and Dual Barcodes With Minimal PCR Amplification Removes Artifacts and Acquires Accurate Antibody Repertoire
title_full_unstemmed Dual UMIs and Dual Barcodes With Minimal PCR Amplification Removes Artifacts and Acquires Accurate Antibody Repertoire
title_short Dual UMIs and Dual Barcodes With Minimal PCR Amplification Removes Artifacts and Acquires Accurate Antibody Repertoire
title_sort dual umis and dual barcodes with minimal pcr amplification removes artifacts and acquires accurate antibody repertoire
topic Immunology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8727365/
https://www.ncbi.nlm.nih.gov/pubmed/35003093
http://dx.doi.org/10.3389/fimmu.2021.778298
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