Anders Roy Christiansen

High-throughput sequencing enhanced phage display enables the identification of patient-specific epitope motifs in serum

Phage display is a prominent screening technique with a multitude of applications including therapeutic antibody development and mapping of antigen epitopes. In this study, phages were selected based on their interaction with patient serum and exhaustively characterised by high-throughput sequencing. A bioinformatics approach was developed in order to identify peptide motifs of interest based on clustering and contrasting to control samples. Comparison of patient and control samples confirmed a major issue in phage display, namely the selection of unspecific peptides. The potential of the bioinformatic approach was demonstrated by identifying epitopes of a prominent peanut allergen, Ara h 1, in sera from patients with severe peanut allergy. The identified epitopes were confirmed by high-density peptide micro-arrays. The present study demonstrates that high-throughput sequencing can empower phage display by (i) enabling the analysis of complex biological samples, (ii) circumventing the traditional laborious picking and functional testing of individual phage clones and (iii) reducing the number of selection rounds.

Linear epitope mapping of peanut allergens demonstrates individualized and persistent antibody-binding patterns

To the Editor: Peanut allergy is considered a major health problem due to its prevalence, persistence, and association with severe symptoms. Previous studies suggest that clinical reactivity to allergens might be related to allergen-specific IgE epitope patterns, diversity, and avidity, all of which likely play a role in the effect of IgE on basophils and mast cells. Previous peptide microarray-based studies have demonstrated a pronounced heterogeneity in the epitopebinding patterns between individual allergic patients apart from a few immunodominant epitopes. Furthermore, elevated IgG4 levels have been associated with protective effects. 8 Here, high-density peptide arrays were applied to map linear IgE and IgG4 epitopes at the single amino acid level. The peptide arrays contained tiled arrays of 12-mer peptides covering the peanut allergens Ara h 1, 2, 3, 6, 8, and 9. Corresponding peptides with alanine substitutions were used to obtain single amino acid resolution of epitopes and their immune reactivity. Maps of IgE and IgG4 reactivity were obtained for 5 control subjects and 6 severely allergic patients (ages 8-40 years) sampled across 4 to 10 years (see Table E1 and the Methods section in this article’s Online Repository at www.jacionline.org).

Compressed Indexing with Signature Grammars

The compressed indexing problem is to preprocess a string

Finger Search in Grammar-Compressed Strings

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Dynamic Relative Compression, Dynamic Partial Sums, and Substring Concatenation

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Succinct Partial Sums and Fenwick Trees

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Parallel Lookups in String Indexes

into a compressed representation that supports pattern matching queries. That is, given a string

Fast Dynamic Arrays

P

Finger Search in Grammar-Compressed Strings.

of length

A novel approach for characterisation of conformational allergen epitopes combining phage display and high-throughput sequencing

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