High-Throughput Sequencing-Based Immune Repertoire Study During Infectious Disease

Overview

Journal Front Immunol

Specialty Allergy & Immunology

Date 2016 Sep 16

PMID 27630639

Citations 28

Authors

Dongni Hou

Cuicui Chen

Eric John Seely

Shujing Chen

Yuanlin Song

Affiliations

Soon will be listed here.

Abstract

The selectivity of the adaptive immune response is based on the enormous diversity of T and B cell antigen-specific receptors. The immune repertoire, the collection of T and B cells with functional diversity in the circulatory system at any given time, is dynamic and reflects the essence of immune selectivity. In this article, we review the recent advances in immune repertoire study of infectious diseases, which were achieved by traditional techniques and high-throughput sequencing (HTS) techniques. HTS techniques enable the determination of complementary regions of lymphocyte receptors with unprecedented efficiency and scale. This progress in methodology enhances the understanding of immunologic changes during pathogen challenge and also provides a basis for further development of novel diagnostic markers, immunotherapies, and vaccines.

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References

Eren M, Chao A, Hwang W, Colwell R . Estimating the richness of a population when the maximum number of classes is fixed: a nonparametric solution to an archaeological problem. PLoS One. 2012; 7(5):e34179. PMC: 3362599. DOI: 10.1371/journal.pone.0034179. View

Gadala-Maria D, Yaari G, Uduman M, Kleinstein S . Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles. Proc Natl Acad Sci U S A. 2015; 112(8):E862-70. PMC: 4345584. DOI: 10.1073/pnas.1417683112. View

Pannetier C, Even J, Kourilsky P . T-cell repertoire diversity and clonal expansions in normal and clinical samples. Immunol Today. 1995; 16(4):176-81. DOI: 10.1016/0167-5699(95)80117-0. View

Quince C, Lanzen A, Curtis T, Davenport R, Hall N, Head I . Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods. 2009; 6(9):639-41. DOI: 10.1038/nmeth.1361. View

Conrad J, Ramalingam R, Duncan C, Smith R, Wei J, Barnett L . Antiretroviral therapy reduces the magnitude and T cell receptor repertoire diversity of HIV-specific T cell responses without changing T cell clonotype dominance. J Virol. 2012; 86(8):4213-21. PMC: 3318638. DOI: 10.1128/JVI.06000-11. View

Giudicelli V, Chaume D, Lefranc M . IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis. Nucleic Acids Res. 2004; 32(Web Server issue):W435-40. PMC: 441550. DOI: 10.1093/nar/gkh412. View

Kwong P, Mascola J . Human antibodies that neutralize HIV-1: identification, structures, and B cell ontogenies. Immunity. 2012; 37(3):412-25. PMC: 4706166. DOI: 10.1016/j.immuni.2012.08.012. View

Wirawan A, Harris R, Liu Y, Schmidt B, Schroder J . HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. BMC Bioinformatics. 2014; 15:131. PMC: 4023493. DOI: 10.1186/1471-2105-15-131. View

Ruggiero E, Nicolay J, Fronza R, Arens A, Paruzynski A, Nowrouzi A . High-resolution analysis of the human T-cell receptor repertoire. Nat Commun. 2015; 6:8081. PMC: 4569693. DOI: 10.1038/ncomms9081. View

10.

Larman H, Xu G, Pavlova N, Elledge S . Construction of a rationally designed antibody platform for sequencing-assisted selection. Proc Natl Acad Sci U S A. 2012; 109(45):18523-8. PMC: 3494914. DOI: 10.1073/pnas.1215549109. View

11.

Jiang N, He J, Weinstein J, Penland L, Sasaki S, He X . Lineage structure of the human antibody repertoire in response to influenza vaccination. Sci Transl Med. 2013; 5(171):171ra19. PMC: 3699344. DOI: 10.1126/scitranslmed.3004794. View

12.

Weinstein J, Jiang N, White 3rd R, Fisher D, Quake S . High-throughput sequencing of the zebrafish antibody repertoire. Science. 2009; 324(5928):807-10. PMC: 3086368. DOI: 10.1126/science.1170020. View

13.

Kao W, Chan A, Song Y . ECHO: a reference-free short-read error correction algorithm. Genome Res. 2011; 21(7):1181-92. PMC: 3129260. DOI: 10.1101/gr.111351.110. View

14.

Ying T, Prabakaran P, Du L, Shi W, Feng Y, Wang Y . Junctional and allele-specific residues are critical for MERS-CoV neutralization by an exceptionally potent germline-like antibody. Nat Commun. 2015; 6:8223. PMC: 4571279. DOI: 10.1038/ncomms9223. View

15.

Turchaninova M, Britanova O, Bolotin D, Shugay M, Putintseva E, Staroverov D . Pairing of T-cell receptor chains via emulsion PCR. Eur J Immunol. 2013; 43(9):2507-15. DOI: 10.1002/eji.201343453. View

16.

Parameswaran P, Liu Y, Roskin K, Jackson K, Dixit V, Lee J . Convergent antibody signatures in human dengue. Cell Host Microbe. 2013; 13(6):691-700. PMC: 4136508. DOI: 10.1016/j.chom.2013.05.008. View

17.

Robinson W . Sequencing the functional antibody repertoire--diagnostic and therapeutic discovery. Nat Rev Rheumatol. 2014; 11(3):171-82. PMC: 4382308. DOI: 10.1038/nrrheum.2014.220. View

18.

Song L, Florea L, Langmead B . Lighter: fast and memory-efficient sequencing error correction without counting. Genome Biol. 2014; 15(11):509. PMC: 4248469. DOI: 10.1186/s13059-014-0509-9. View

19.

Munshaw S, Kepler T . SoDA2: a Hidden Markov Model approach for identification of immunoglobulin rearrangements. Bioinformatics. 2010; 26(7):867-72. PMC: 2844993. DOI: 10.1093/bioinformatics/btq056. View

20.

Yang X, Chockalingam S, Aluru S . A survey of error-correction methods for next-generation sequencing. Brief Bioinform. 2012; 14(1):56-66. DOI: 10.1093/bib/bbs015. View