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Phage Immunoprecipitation Sequencing (PhIP-Seq) for Analyzing Antibody Epitope Repertoires Against Food Antigens

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Food Allergens

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2717))

Abstract

While thousands of food and environmental allergens have been reported, conventional methods for allergy testing typically rely on measuring immunoglobulin E (IgE) binding against panels of dozens to hundreds of antigens. Beyond IgE, also the specificity of other Ig (sub-)classes such as IgG4, has gained interest because of a potential protective role toward allergy.

Phage immunoprecipitation sequencing (PhIP-Seq) allows to study hundreds of thousands of rationally selected peptide antigens and to resolve binding specificities of different Ig classes. This technology combines synthetic DNA libraries encoding antigens, with the display on the surface of T7 bacteriophages and next-generation sequencing (NGS) for quantitative readouts. Thereby binding of entire Ig repertoires can be measured to detect the exact epitopes of food allergens and to study potential cross-reactivity.

In this chapter, we provide a summary of both the key experimental steps and various strategies for analyzing PhIP-Seq datasets, as well as comparing the advantages and disadvantages of this methodology for measuring antibody responses against food antigens.

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  1. Ioanna Filimonova and Gabriel Innocenti contributed equally with all other contributors.

Authors and Affiliations

  1. Medical University of Vienna, Center for Cancer Research, Vienna, Austria

    Ioanna Filimonova, Gabriel Innocenti & Thomas Vogl

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  1. Ioanna Filimonova
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  2. Gabriel Innocenti
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  3. Thomas Vogl
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Correspondence to Thomas Vogl .

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Editors and Affiliations

  1. Department of Allergy, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain

    Beatriz Cabanillas

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Filimonova, I., Innocenti, G., Vogl, T. (2024). Phage Immunoprecipitation Sequencing (PhIP-Seq) for Analyzing Antibody Epitope Repertoires Against Food Antigens. In: Cabanillas, B. (eds) Food Allergens. Methods in Molecular Biology, vol 2717. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3453-0_7

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  • DOI: https://doi.org/10.1007/978-1-0716-3453-0_7

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