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Related Experiment Video

Updated: Nov 20, 2025

Identification of Mouse and Human Antibody Repertoires by Next-Generation Sequencing
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bbeaR: an R package and framework for epitope-specific antibody profiling.

Maria Suprun1, Randall J Ellis2, Hugh A Sampson1

  • 1Department of Pediatrics, Allergy and Immunology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

Bioinformatics (Oxford, England)
|January 20, 2021
PubMed
Summary
This summary is machine-generated.

A new Bead-Based Epitope Assay (BBEA) and its R package, bbeaR, enable detailed analysis of epitope-specific antibodies for understanding inflammatory disorders like allergies.

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Area of Science:

  • Immunology
  • Bioinformatics

Background:

  • Inflammatory disorders, particularly allergies, are increasingly understood through epitope-specific antibody repertoires.
  • Quantifying these antibody levels is crucial for elucidating disease pathogenesis.

Purpose of the Study:

  • To introduce a novel multiplex immunoassay, the Bead-Based Epitope Assay (BBEA).
  • To present bbeaR, an open-source R package designed for comprehensive analysis of BBEA data.

Main Methods:

  • Development of the Bead-Based Epitope Assay (BBEA) for quantifying epitope-specific immunoglobulins (IgE, IgG, IgA, IgD).
  • Creation of the bbeaR R package to process, normalize, and analyze Luminex reader data.
  • Implementation of quality control, differential antibody analysis, and epitope sequence mapping within bbeaR.

Main Results:

  • The bbeaR package facilitates the import, processing, and normalization of .csv data from Luminex readers.
  • It allows for robust quality control assessment and differential analysis of epitope-binding antibodies using linear modeling.
  • Results can be visualized, and epitope sequences can be mapped to primary protein structures.

Conclusions:

  • The BBEA and bbeaR package offer a streamlined and reproducible framework for analyzing epitope-specific antibody profiles.
  • This approach provides novel insights into the pathogenesis of inflammatory disorders, especially allergies.
  • The open-source nature of bbeaR promotes accessibility and further research in the field.