title: High-throughput sequencing enhanced phage display enables the identification of patient-specific epitope motifs in serum.
abstract: 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.
authors.affiliation: Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Anders
authors.initials: A
authors.lastname: Christiansen
authors.affiliation: Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Jens V
authors.initials: JV
authors.lastname: Kringelum
authors.affiliation: Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Christian S
authors.initials: CS
authors.lastname: Hansen
authors.affiliation: National Food Institute, Technical University of Denmark, Søborg, Denmark.
authors.forename: Katrine L
authors.initials: KL
authors.lastname: Bøgh
authors.affiliation: Roche NimbleGen, Madison, Wisconsin, the United States of America.
authors.forename: Eric
authors.initials: E
authors.lastname: Sullivan
authors.affiliation: Roche NimbleGen, Madison, Wisconsin, the United States of America.
authors.forename: Jigar
authors.initials: J
authors.lastname: Patel
authors.affiliation: Institute of Food Research, Norwich, United Kingdom.
authors.forename: Neil M
authors.initials: NM
authors.lastname: Rigby
authors.affiliation: Department of Paediatrics, Medical University of Vienna, Vienna, Austria.
authors.forename: Thomas
authors.initials: T
authors.lastname: Eiwegger
authors.affiliation: Department of Paediatrics, Medical University of Vienna, Vienna, Austria.
authors.forename: Zsolt
authors.initials: Z
authors.lastname: Szépfalusi
authors.affiliation: Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Federico
authors.initials: F
authors.lastname: de Masi
authors.affiliation: 1] Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark [2] Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina.
authors.forename: Morten
authors.initials: M
authors.lastname: Nielsen
authors.affiliation: Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Ole
authors.initials: O
authors.lastname: Lund
authors.affiliation: Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Martin
authors.initials: M
authors.lastname: Dufva
mesh_terms: D020816:Amino Acid Motifs; D000939:Epitopes / Q000097:blood / Q000235:genetics; D005260:Female; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D021183:Peanut Hypersensitivity / Q000097:blood / Q000235:genetics; D040081:Protein Array Analysis
chemical_list: D000939:Epitopes