ArticleJournal of immunology (Baltimore, Md. : 1950)2017
Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads.
Article in Journal of immunology (Baltimore, Md. : 1950), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Estimates of Sequences with Ultralong and Short CDR3s in the Bovine IgM B Cell Receptor Repertoire Using the Long-read Oxford Nanopore MinION Platform.ImmunoHorizons · 2024Article
- nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework.PLoS computational biology · 2024Article
- Extraction of the CDRH3 sequence of the mouse antibody repertoire selected upon influenza virus infection by subtraction of the background antibody repertoire.Journal of virology · 2024Article
- Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires.Nucleic acids research · 2023Article
- Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques.Science translational medicine · 2022Article
- Targeted isolation of diverse human protective broadly neutralizing antibodies against SARS-like viruses.Nature immunology · 2022Article
- Antibody repertoire sequencing analysis.Acta biochimica et biophysica Sinica · 2022Review
- Variations in antibody repertoires correlate with vaccine responses.Genome research · 2022Article
- Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause severe disease.bioRxiv : the preprint server for biology · 2022Article
- Targeted isolation of panels of diverse human protective broadly neutralizing antibodies against SARS-like viruses.bioRxiv : the preprint server for biology · 2022Article
- A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods.Frontiers in immunology · 2022Article
- Next Generation Sequencing of Cerebrospinal Fluid B Cell Repertoires in Multiple Sclerosis and Other Neuro-Inflammatory Diseases-A Comprehensive Review.Diagnostics (Basel, Switzerland) · 2021Review
- Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor naïve human B cells.NPJ vaccines · 2021Article
- B cell engagement with HIV-1 founder virus envelope predicts development of broadly neutralizing antibodies.Cell host & microbe · 2021Article
- V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s.Genome research · 2020Article
- Computational approaches to therapeutic antibody design: established methods and emerging trends.Briefings in bioinformatics · 2020Review
- Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species.PLoS computational biology · 2020Article
- A comparison of unamplified and massively multiplexed PCR amplification for murine antibody repertoire sequencing.FASEB bioAdvances · 2019Article
- A comparison of unamplified and massively multiplexed PCR amplification for murine antibody repertoire sequencing.FASEB bioAdvances · 2019Article
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Authors and funding
6 authors.
Funding
Abstract
Transforming error-prone immunosequencing datasets into Ab repertoires is a fundamental problem in immunogenomics, and a prerequisite for studies of immune responses. Although various repertoire reconstruction algorithms were released in the last 3 y, it remains unclear how to benchmark them and how to assess the accuracy of the reconstructed repertoires. We describe an accurate IgReC algorithm for constructing Ab repertoires from high-throughput immunosequencing datasets and a new framework for assessing the quality of reconstructed repertoires. Surprisingly, Ab repertoires constructed by IgReC from barcoded immunosequencing datasets in the blind mode (without using information about unique molecular identifiers) improved upon the repertoires constructed by the state-of-the-art tools that use barcoding. This finding suggests that IgReC may alleviate the need to generate repertoires using the barcoding technology (the workhorse of current immunogenomics efforts) because our computational approach to error correction of immunosequencing data is nearly as powerful as the experimental approach based on barcoding.
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