Literature DB >> 27065089

Deep sequencing and human antibody repertoire analysis.

Scott D Boyd1, James E Crowe2.   

Abstract

In the past decade, high-throughput DNA sequencing (HTS) methods and improved approaches for isolating antigen-specific B cells and their antibody genes have been applied in many areas of human immunology. This work has greatly increased our understanding of human antibody repertoires and the specific clones responsible for protective immunity or immune-mediated pathogenesis. Although the principles underlying selection of individual B cell clones in the intact immune system are still under investigation, the combination of more powerful genetic tracking of antibody lineage development and functional testing of the encoded proteins promises to transform therapeutic antibody discovery and optimization. Here, we highlight recent advances in this fast-moving field.
Copyright © 2016. Published by Elsevier Ltd.

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Year:  2016        PMID: 27065089      PMCID: PMC5203765          DOI: 10.1016/j.coi.2016.03.008

Source DB:  PubMed          Journal:  Curr Opin Immunol        ISSN: 0952-7915            Impact factor:   7.486


  31 in total

1.  IMGT(®) tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS.

Authors:  Eltaf Alamyar; Patrice Duroux; Marie-Paule Lefranc; Véronique Giudicelli
Journal:  Methods Mol Biol       Date:  2012

2.  Effects of aging, cytomegalovirus infection, and EBV infection on human B cell repertoires.

Authors:  Chen Wang; Yi Liu; Lan T Xu; Katherine J L Jackson; Krishna M Roskin; Tho D Pham; Jonathan Laserson; Eleanor L Marshall; Katie Seo; Ji-Yeun Lee; David Furman; Daphne Koller; Cornelia L Dekker; Mark M Davis; Andrew Z Fire; Scott D Boyd
Journal:  J Immunol       Date:  2013-12-11       Impact factor: 5.422

3.  Somatic mutations of the immunoglobulin framework are generally required for broad and potent HIV-1 neutralization.

Authors:  Florian Klein; Ron Diskin; Johannes F Scheid; Christian Gaebler; Hugo Mouquet; Ivelin S Georgiev; Marie Pancera; Tongqing Zhou; Reha-Baris Incesu; Brooks Zhongzheng Fu; Priyanthi N P Gnanapragasam; Thiago Y Oliveira; Michael S Seaman; Peter D Kwong; Pamela J Bjorkman; Michel C Nussenzweig
Journal:  Cell       Date:  2013-03-28       Impact factor: 41.582

4.  Timely and spatially regulated maturation of B and T cell repertoire during human fetal development.

Authors:  Erez Rechavi; Atar Lev; Yu Nee Lee; Amos J Simon; Yoav Yinon; Schlomo Lipitz; Ninette Amariglio; Boaz Weisz; Luigi D Notarangelo; Raz Somech
Journal:  Sci Transl Med       Date:  2015-02-25       Impact factor: 17.956

5.  B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes.

Authors:  Joel N H Stern; Gur Yaari; Jason A Vander Heiden; George Church; William F Donahue; Rogier Q Hintzen; Anita J Huttner; Jon D Laman; Rashed M Nagra; Alyssa Nylander; David Pitt; Sriram Ramanan; Bilal A Siddiqui; Francois Vigneault; Steven H Kleinstein; David A Hafler; Kevin C O'Connor
Journal:  Sci Transl Med       Date:  2014-08-06       Impact factor: 17.956

Review 6.  Diagnostic applications of high-throughput DNA sequencing.

Authors:  Scott D Boyd
Journal:  Annu Rev Pathol       Date:  2012-11-01       Impact factor: 23.472

7.  Convergent antibody signatures in human dengue.

Authors:  Poornima Parameswaran; Yi Liu; Krishna M Roskin; Katherine K L Jackson; Vaishali P Dixit; Ji-Yeun Lee; Karen L Artiles; Simona Zompi; Maria José Vargas; Birgitte B Simen; Bozena Hanczaruk; Kim R McGowan; Muhammad A Tariq; Nader Pourmand; Daphne Koller; Angel Balmaseda; Scott D Boyd; Eva Harris; Andrew Z Fire
Journal:  Cell Host Microbe       Date:  2013-06-12       Impact factor: 21.023

8.  Molecular ontogeny of the human antibody repertoire to the Haemophilus influenzae type B polysaccharide: expression of canonical variable regions and their variants in vaccinated infants.

Authors:  Alexander H Lucas; Gary R McLean; Donald C Reason; Adam P O'Connor; Mistique C Felton; Karen D Moulton
Journal:  Clin Immunol       Date:  2003-08       Impact factor: 3.969

9.  Individual variation in the germline Ig gene repertoire inferred from variable region gene rearrangements.

Authors:  Scott D Boyd; Bruno A Gaëta; Katherine J Jackson; Andrew Z Fire; Eleanor L Marshall; Jason D Merker; Jay M Maniar; Lyndon N Zhang; Bita Sahaf; Carol D Jones; Birgitte B Simen; Bozena Hanczaruk; Khoa D Nguyen; Kari C Nadeau; Michael Egholm; David B Miklos; James L Zehnder; Andrew M Collins
Journal:  J Immunol       Date:  2010-05-21       Impact factor: 5.422

10.  Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity.

Authors:  Corey T Watson; Karyn Meltz Steinberg; Tina A Graves; Rene L Warren; Maika Malig; Jacqueline Schein; Richard K Wilson; Robert A Holt; Evan E Eichler; Felix Breden
Journal:  Genes Immun       Date:  2014-10-23       Impact factor: 2.676

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  18 in total

1.  The Extended Impact of Human Immunodeficiency Virus/AIDS Research.

Authors:  Tara A Schwetz; Anthony S Fauci
Journal:  J Infect Dis       Date:  2019-01-01       Impact factor: 5.226

2.  In Silico Prediction Analysis of Idiotope-Driven T-B Cell Collaboration in Multiple Sclerosis.

Authors:  Rune A Høglund; Andreas Lossius; Jorunn N Johansen; Jane Homan; Jūratė Šaltytė Benth; Harlan Robins; Bjarne Bogen; Robert D Bremel; Trygve Holmøy
Journal:  Front Immunol       Date:  2017-10-02       Impact factor: 7.561

3.  Rare, high-affinity anti-pathogen antibodies from human repertoires, discovered using microfluidics and molecular genomics.

Authors:  Adam S Adler; Rena A Mizrahi; Matthew J Spindler; Matthew S Adams; Michael A Asensio; Robert C Edgar; Jackson Leong; Renee Leong; Lucy Roalfe; Rebecca White; David Goldblatt; David S Johnson
Journal:  MAbs       Date:  2017-08-28       Impact factor: 5.857

4.  Next-Generation Immune Repertoire Sequencing as a Clue to Elucidate the Landscape of Immune Modulation by Host-Gut Microbiome Interactions.

Authors:  Tatsuo Ichinohe; Takahiko Miyama; Takakazu Kawase; Yasuko Honjo; Kazutaka Kitaura; Hiroyuki Sato; Tadasu Shin-I; Ryuji Suzuki
Journal:  Front Immunol       Date:  2018-04-03       Impact factor: 7.561

Review 5.  Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires.

Authors:  Enkelejda Miho; Alexander Yermanos; Cédric R Weber; Christoph T Berger; Sai T Reddy; Victor Greiff
Journal:  Front Immunol       Date:  2018-02-21       Impact factor: 7.561

Review 6.  Immunoglobulin gene analysis as a tool for investigating human immune responses.

Authors:  Deborah Dunn-Walters; Catherine Townsend; Emma Sinclair; Alex Stewart
Journal:  Immunol Rev       Date:  2018-07       Impact factor: 12.988

7.  Antibody Heavy Chain Variable Domains of Different Germline Gene Origins Diversify through Different Paths.

Authors:  Ufuk Kirik; Helena Persson; Fredrik Levander; Lennart Greiff; Mats Ohlin
Journal:  Front Immunol       Date:  2017-11-13       Impact factor: 7.561

8.  Antigen receptor repertoire profiling from RNA-seq data.

Authors:  Dmitriy A Bolotin; Stanislav Poslavsky; Alexey N Davydov; Felix E Frenkel; Lorenzo Fanchi; Olga I Zolotareva; Saskia Hemmers; Ekaterina V Putintseva; Anna S Obraztsova; Mikhail Shugay; Ravshan I Ataullakhanov; Alexander Y Rudensky; Ton N Schumacher; Dmitriy M Chudakov
Journal:  Nat Biotechnol       Date:  2017-10-11       Impact factor: 54.908

Review 9.  Advances in Electrochemical and Acoustic Aptamer-Based Biosensors and Immunosensors in Diagnostics of Leukemia.

Authors:  Tibor Hianik
Journal:  Biosensors (Basel)       Date:  2021-05-31

Review 10.  Computational Modeling of Hepatitis C Virus Envelope Glycoprotein Structure and Recognition.

Authors:  Johnathan D Guest; Brian G Pierce
Journal:  Front Immunol       Date:  2018-05-28       Impact factor: 7.561

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