Deep Panning: steps towards probing the IgOme.

<h4>Background</h4>Polyclonal serum consists of vast collections of antibodies, products of differentiated B-cells. The spectrum of antibody specificities is dynamic and varies with age, physiology, and exposure to pathological insults. The complete repertoire of antibody specificities i...

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Autores principales:	Arie Ryvkin, Haim Ashkenazy, Larisa Smelyanski, Gilad Kaplan, Osnat Penn, Yael Weiss-Ottolenghi, Eyal Privman, Peter B Ngam, James E Woodward, Gregory D May, Callum Bell, Tal Pupko, Jonathan M Gershoni
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9f0f357ef11241da9aec6ce6f119a71e
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id	oai:doaj.org-article:9f0f357ef11241da9aec6ce6f119a71e
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spelling	oai:doaj.org-article:9f0f357ef11241da9aec6ce6f119a71e2021-11-18T07:10:09ZDeep Panning: steps towards probing the IgOme.1932-620310.1371/journal.pone.0041469https://doaj.org/article/9f0f357ef11241da9aec6ce6f119a71e2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22870226/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Polyclonal serum consists of vast collections of antibodies, products of differentiated B-cells. The spectrum of antibody specificities is dynamic and varies with age, physiology, and exposure to pathological insults. The complete repertoire of antibody specificities in blood, the IgOme, is therefore an extraordinarily rich source of information-a molecular record of previous encounters as well as a status report of current immune activity. The ability to profile antibody specificities of polyclonal serum at exceptionally high resolution has been an important and serious challenge which can now be overcome.<h4>Methodology/principal findings</h4>Here we illustrate the application of Deep Panning, a method that combines the flexibility of combinatorial phage display of random peptides with the power of high-throughput deep sequencing. Deep Panning is first applied to evaluate the quality and diversity of naïve random peptide libraries. The production of very large data sets, hundreds of thousands of peptides, has revealed unexpected properties of combinatorial random peptide libraries and indicates correctives to ensure the quality of the libraries generated. Next, Deep Panning is used to analyze a model monoclonal antibody in addition to allowing one to follow the dynamics of biopanning and peptide selection. Finally Deep Panning is applied to profile polyclonal sera derived from HIV infected individuals.<h4>Conclusions/significance</h4>The ability to generate and characterize hundreds of thousands of affinity-selected peptides creates an effective means towards the interrogation of the IgOme and understanding of the humoral response to disease. Deep Panning should open the door to new possibilities for serological diagnostics, vaccine design and the discovery of the correlates of immunity to emerging infectious agents.Arie RyvkinHaim AshkenazyLarisa SmelyanskiGilad KaplanOsnat PennYael Weiss-OttolenghiEyal PrivmanPeter B NgamJames E WoodwardGregory D MayCallum BellTal PupkoJonathan M GershoniPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 8, p e41469 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Arie Ryvkin Haim Ashkenazy Larisa Smelyanski Gilad Kaplan Osnat Penn Yael Weiss-Ottolenghi Eyal Privman Peter B Ngam James E Woodward Gregory D May Callum Bell Tal Pupko Jonathan M Gershoni Deep Panning: steps towards probing the IgOme.
description	<h4>Background</h4>Polyclonal serum consists of vast collections of antibodies, products of differentiated B-cells. The spectrum of antibody specificities is dynamic and varies with age, physiology, and exposure to pathological insults. The complete repertoire of antibody specificities in blood, the IgOme, is therefore an extraordinarily rich source of information-a molecular record of previous encounters as well as a status report of current immune activity. The ability to profile antibody specificities of polyclonal serum at exceptionally high resolution has been an important and serious challenge which can now be overcome.<h4>Methodology/principal findings</h4>Here we illustrate the application of Deep Panning, a method that combines the flexibility of combinatorial phage display of random peptides with the power of high-throughput deep sequencing. Deep Panning is first applied to evaluate the quality and diversity of naïve random peptide libraries. The production of very large data sets, hundreds of thousands of peptides, has revealed unexpected properties of combinatorial random peptide libraries and indicates correctives to ensure the quality of the libraries generated. Next, Deep Panning is used to analyze a model monoclonal antibody in addition to allowing one to follow the dynamics of biopanning and peptide selection. Finally Deep Panning is applied to profile polyclonal sera derived from HIV infected individuals.<h4>Conclusions/significance</h4>The ability to generate and characterize hundreds of thousands of affinity-selected peptides creates an effective means towards the interrogation of the IgOme and understanding of the humoral response to disease. Deep Panning should open the door to new possibilities for serological diagnostics, vaccine design and the discovery of the correlates of immunity to emerging infectious agents.
format	article
author	Arie Ryvkin Haim Ashkenazy Larisa Smelyanski Gilad Kaplan Osnat Penn Yael Weiss-Ottolenghi Eyal Privman Peter B Ngam James E Woodward Gregory D May Callum Bell Tal Pupko Jonathan M Gershoni
author_facet	Arie Ryvkin Haim Ashkenazy Larisa Smelyanski Gilad Kaplan Osnat Penn Yael Weiss-Ottolenghi Eyal Privman Peter B Ngam James E Woodward Gregory D May Callum Bell Tal Pupko Jonathan M Gershoni
author_sort	Arie Ryvkin
title	Deep Panning: steps towards probing the IgOme.
title_short	Deep Panning: steps towards probing the IgOme.
title_full	Deep Panning: steps towards probing the IgOme.
title_fullStr	Deep Panning: steps towards probing the IgOme.
title_full_unstemmed	Deep Panning: steps towards probing the IgOme.
title_sort	deep panning: steps towards probing the igome.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/9f0f357ef11241da9aec6ce6f119a71e
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Deep Panning: steps towards probing the IgOme.

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