ArticlePhilosophical transactions of the Royal Society of London. Series B, Biological sciences2015
Assigning and visualizing germline genes in antibody repertoires.
Article in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Unmutated IGHV1-69 CLL Clone Displays a Distinct Gene Expression Profile by a Comparative qRT-PCR Assay.Biomedicines · 2022Article
- Pan-neutralizing, germline-encoded antibodies against SARS-CoV-2: Addressing the long-term problem of escape variants.Frontiers in immunology · 2022Article
- How repertoire data are changing antibody science.The Journal of biological chemistry · 2020Review
- The replication-competent HIV-1 latent reservoir is primarily established near the time of therapy initiation.Science translational medicine · 2019Article
- DSab-origin: a novel IGHD sensitive VDJ mapping method and its application on antibody response after influenza vaccination.BMC bioinformatics · 2019Article
- Analyzing Immunoglobulin Repertoires.Frontiers in immunology · 2018Review
- Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses.Frontiers in immunology · 2017Article
- Likelihood-Based Inference of B Cell Clonal Families.PLoS computational biology · 2016Article
- repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data.Bioinformatics (Oxford, England) · 2016Article
- The Diversity and Molecular Evolution of B-Cell Receptors during Infection.Molecular biology and evolution · 2016Review
- BRILIA: Integrated Tool for High-Throughput Annotation and Lineage Tree Assembly of B-Cell Repertoires.Frontiers in immunology · 2016Article
- Practical guidelines for B-cell receptor repertoire sequencing analysis.Genome medicine · 2015Review
- The evolution within us.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2015Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Identifying the germline genes involved in immunoglobulin rearrangements is an essential first step in the analysis of antibody repertoires. Based on our prior work in analysing diverse recombinant viruses, we present IgSCUEAL (Immunoglobulin Subtype Classification Using Evolutionary ALgorithms), a phylogenetic approach to assign V and J regions of immunoglobulin sequences to their corresponding germline alleles, with D regions assigned using a simple pairwise alignment algorithm. We also develop an interactive web application for viewing the results, allowing the user to explore the frequency distribution of sequence assignments and CDR3 region length statistics, which is useful for summarizing repertoires, as well as a detailed viewer of rearrangements and region alignments for individual query sequences. We demonstrate the accuracy and utility of our method compared with sequence similarity-based approaches and other non-phylogenetic model-based approaches, using both simulated data and a set of evaluation datasets of human immunoglobulin heavy chain sequences. IgSCUEAL demonstrates the highest accuracy of V and J assignment amongst existing approaches, even when the reassorted sequence is highly mutated, and can successfully cluster sequences on the basis of shared V/J germline alleles.
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