Maria Suprun1, Randall J Ellis2, Hugh A Sampson1, Mayte Suárez-Fariñas3,4. 1. Department of Pediatrics, Allergy and Immunology. 2. Addiction Institute of Mount Sinai. 3. Department of Population Health Science and Policy. 4. Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Abstract
SUMMARY: Analysis of epitope-specific antibody repertoires has provided novel insights into the pathogenesis of inflammatory disorders, especially allergies. A novel multiplex immunoassay, termed Bead-Based Epitope Assay (BBEA), was developed to quantify levels of epitope-specific immunoglobulins, including IgE, IgG, IgA and IgD isotypes. bbeaR is an open-source R package, developed for the BBEA, provides a framework to import, process and normalize .csv data files exported from the Luminex reader, evaluate various quality control metrics, analyze differential epitope-binding antibodies with linear modelling, visualize results, and map epitopes' amino acid sequences to their respective primary protein structures. bbeaR enables streamlined and reproducible analysis of epitope-specific antibody profiles. AVAILABILITY AND IMPLEMENTATION: bbeaR is open-source and freely available from GitHub as an R package: https://github.com/msuprun/bbeaR; vignettes included. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: Analysis of epitope-specific antibody repertoires has provided novel insights into the pathogenesis of inflammatory disorders, especially allergies. A novel multiplex immunoassay, termed Bead-Based Epitope Assay (BBEA), was developed to quantify levels of epitope-specific immunoglobulins, including IgE, IgG, IgA and IgD isotypes. bbeaR is an open-source R package, developed for the BBEA, provides a framework to import, process and normalize .csv data files exported from the Luminex reader, evaluate various quality control metrics, analyze differential epitope-binding antibodies with linear modelling, visualize results, and map epitopes' amino acid sequences to their respective primary protein structures. bbeaR enables streamlined and reproducible analysis of epitope-specific antibody profiles. AVAILABILITY AND IMPLEMENTATION: bbeaR is open-source and freely available from GitHub as an R package: https://github.com/msuprun/bbeaR; vignettes included. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Alexandra F Santos; Nuno L Barbosa-Morais; Barry K Hurlburt; Sneha Ramaswamy; Oliver Hemmings; Matthew Kwok; Colin O'Rourke; Henry T Bahnson; Hsiaopo Cheng; Louisa James; Hannah J Gould; Brian J Sutton; Soheila J Maleki; Gideon Lack Journal: Allergy Date: 2020-04-23 Impact factor: 13.146