Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2019 Apr 30:10:899.
doi: 10.3389/fimmu.2019.00899. eCollection 2019.

The Pipeline Repertoire for Ig-Seq Analysis

Laura López-Santibáñez-Jácome  1   2 , S Eréndira Avendaño-Vázquez  1 , Carlos Fabián Flores-Jasso  1
Affiliations
Review

The Pipeline Repertoire for Ig-Seq Analysis

Laura López-Santibáñez-Jácome et al. Front Immunol. .

Abstract

With the advent of high-throughput sequencing of immunoglobulin genes (Ig-Seq), the understanding of antibody repertoires and their dynamics among individuals and populations has become an exciting area of research. There is an increasing number of computational tools that aid in every step of the immune repertoire characterization. However, since not all tools function identically, every pipeline has its unique rationale and capabilities, creating a rich blend of useful features that may appear intimidating for newcomer laboratories with the desire to plunge into immune repertoire analysis to expand and improve their research; hence, all pipeline strengths and differences may not seem evident. In this review we provide a practical and organized list of the current set of computational tools, focusing on their most attractive features and differences in order to carry out the characterization of antibody repertoires so that the reader better decides a strategic approach for the experimental design, and computational pathways for the analyses of immune repertoires.

Keywords: Ig-Seq; V(D)J alignment; antibody repertoire; pipeline; pre-processing.

PubMed Disclaimer

References

    1. Georgiou G, Ippolito GC, Beausang J, Busse CE, Wardemann H, Quake SR. The promise and challenge of high-throughput sequencing of the antibody repertoire. Nat Biotechnol. (2014) 32:158–68. 10.1038/nbt.2782 - DOI - PMC - PubMed
    1. Miho E, Yermanos A, Weber CR, Berger CT, Reddy ST, Greiff V. Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires. Front Immunol. (2018) 9:224. 10.3389/fimmu.2018.00224 - DOI - PMC - PubMed
    1. Jiang N, He J, Weinstein JA, Penland L, Sasaki S, He XS, et al. . Lineage structure of the human antibody repertoire in response to influenza vaccination. Sci Transl Med. (2013) 5:171ra19. 10.1126/scitranslmed.3004794 - DOI - PMC - PubMed
    1. Yaari G, Benichou JIC, Vander Heiden JA, Kleinstein SH, Louzoun Y. The mutation patterns in B-cell immunoglobulin receptors reflect the influence of selection acting at multiple time-scales. Philos Trans R Soc B Biol Sci. (2015) 370:20140242. 10.1098/rstb.2014.0242 - DOI - PMC - PubMed
    1. Yermanos A, Greiff V, Krautler NJ, Menzel U, Dounas A, Miho E, et al. . Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim). Bioinformatics. (2017) 33:3938–46. 10.1093/bioinformatics/btx533 - DOI - PubMed

Publication types

Substances