ArticleGenes and immunity2012
Location and length distribution of somatic hypermutation-associated DNA insertions and deletions reveals regions of antibody structural plasticity.
Article in Genes and immunity, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
52 citing papers in PubMed, 76 citations in OpenAlex.
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- Antibody Affinity Maturation by Computational Design.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Explore antibody repertoire in the era of AI.Acta biochimica et biophysica Sinica · 2025Article
- Identification of a broad and potent V3 glycan site bNAb targeting an N332bioRxiv : the preprint server for biology · 2025Article
- Scifer: An R/Bioconductor package for large-scale integration of Sanger sequencing and flow cytometry data of index-sorted single cells.Immunoinformatics (Amsterdam, Netherlands) · 2024Article
- MICA-specific nanobodies for diagnosis and immunotherapy of MICAFrontiers in immunology · 2024Article
- Fast clonal family inference from large-scale B cell repertoire sequencing data.Cell reports methods · 2023Article
- Signatures of VNature communications · 2023Article
- Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies.PLoS pathogens · 2023Article
- DNA repair mechanisms that promote insertion-deletion events during immunoglobulin gene diversification.Science immunology · 2023Article
- Applications of High-Throughput DNA Sequencing to Single-Domain Antibody Discovery and Engineering.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A multi-objective based clustering for inferring BCR clonal lineages from high-throughput B cell repertoire data.PLoS computational biology · 2022Article
- Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies.PLoS computational biology · 2022Article
- Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis.Methods in molecular biology (Clifton, N.J.) · 2022Article
- How Antibodies Recognize Pathogenic Viruses: Structural Correlates of Antibody Neutralization of HIV-1, SARS-CoV-2, and Zika.Viruses · 2021Review
- In vitro evolution of antibody affinity via insertional scanning mutagenesis of an entire antibody variable region.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST.BMC bioinformatics · 2020Article
- Targeting the N332-supersite of the HIV-1 envelope for vaccine design.Expert opinion on therapeutic targets · 2020Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Following the initial diversity generated by V(D)J recombination, somatic hypermutation is the principal mechanism for producing further antibody repertoire diversity in antigen-experienced B cells. While somatic hypermutation typically results in single-nucleotide substitutions, the infrequent incorporation of genetic insertions and deletions has also been associated with the somatic hypermutation process. We used high-throughput antibody sequencing to determine the sequence of thousands of antibody genes containing somatic hypermutation-associated insertions and deletions (SHA indels), which revealed significant differences between the location of SHA indels and somatic mutations. Further, we identified a cluster of insertions and deletions in the antibody framework 3 region, which corresponds to the hypervariable region 4 (HV4) in T-cell receptors. We propose that this HV4-like region, identified by SHA indel analysis, represents a region of under-appreciated affinity maturation potential. Finally, through the analysis of both location and length distribution of SHA indels, we have determined regions of structural plasticity within the antibody protein.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.