Cited by 243T-cell and B-cell Immunologyvaccines and immunoinformatics approachesArtificial Immune Systems Applications

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Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires

Greiff, Victor, Miho, Enkelejda, Menzel, Ulrike, Reddy, Sai T.·2015·Trends in Immunology

DOI 10.1016/j.it.2015.09.006

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Abstract

High-throughput sequencing (HTS) of immune repertoires has enabled the quantitative analysis of adaptive immune responses and offers the potential to revolutionize research in lymphocyte biology, vaccine profiling, and monoclonal antibody engineering. Advances in sequencing technology coupled to an exponential decline in sequencing costs have fueled the recent overwhelming interest in immune repertoire sequencing. This, in turn, has sparked the development of numerous methods for bioinformatic and statistics-driven interpretation and visualization of immune repertoires. Here, we review the current literature on bioinformatic and statistical analysis of immune repertoire HTS data and discuss underlying assumptions, applicability, and scope. We further highlight important directions for future research, which could propel immune repertoire HTS to becoming a standard method for measuring adaptive immune responses.

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Additional file 6 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
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Additional file 27 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691697
Additional file 10 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691646
Additional file 18 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691670
Additional file 37 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691727
Additional file 12 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
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Additional file 5 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691631
Additional file 2 of Systematic evaluation of B-cell clonal family inference approaches
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Self-citation
Additional file 1 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25389502
Additional file 2 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25389926
Additional file 24 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691688
Additional file 14 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691658
Additional file 15 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691661
Additional file 26 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691694
Additional file 13 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691655
Additional file 25 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691691
Additional file 39 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691736
Additional file 4 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., Lasanta, M. L., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691625
Additional file 21 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691679
Additional file 8 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691640
Additional file 20 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691676
Additional file 38 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., Lasanta, M. L., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691733
Additional file 30 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691706
Additional file 32 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., Lasanta, M. L., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Sánchez-Fernández, S. Á., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691712
Additional file 1 of Systematic evaluation of B-cell clonal family inference approaches
Balashova, D., van Schaik, B. D. C., Stratigopoulou, M., Guikema, J. E. J., Caniels, T. G., Claireaux, M. A. F., van Gils, M. J., Musters, A., Anang, D. C., de Vries, N., et al. (2024) · Figshare · doi:10.6084/m9.figshare.25194818
Self-citation
Additional file 40 of Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes
Aterido, A., López-Lasanta, M., Blanco, F. J., Juan-Mas, A., García-Vivar, M. L., Erra, A., Pérez-García, C., Fernandez, S. S., Sanmartí, R., Fernández‐Nebro, A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26691739
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FAIRsharing record for: Minimal information about Adaptive Immune Receptor Repertoire
FAIRsharing Team, Kleinstein, S. H., & Busse, C. (2018) · FAIRsharing.org · doi:10.25504/fairsharing.31hec1

Authors: Greiff, V., Miho, E., Menzel, U., & Reddy, S. T.
Affiliations: ETH Zurich (CH)
Corresponding author: Reddy, Sai T.
ORCID: Greiff, Victor
Miho, Enkelejda
Reddy, Sai T.
Venue: Trends in Immunology
Publisher: Elsevier BV
Published: 2015-11
Volume: 36
Issue: 11
Pages: 738-749
ISSN: 1471-4906 (ISSN-L)
DOI: 10.1016/j.it.2015.09.006
OpenAlex: W1883768105
Cited by: 210
References: 132
Citations by year: 2026: 17 · 2025: 17 · 2024: 26 · 2023: 15 · 2022: 28 · 2021: 23 · 2020: 26 · 2019: 14 · 2018: 15 · 2017: 17 · 2016: 12
FWCI: 1.42
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Trends in Immunology (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
Physical Sciences › Computer Science › Artificial Intelligence › Artificial Immune Systems Applications
Keywords: immune repertoire sequencing, adaptive immune response, bioinformatics analysis, statistical analysis, B cell receptor repertoire, T cell receptor repertoire, lymphocyte biology
MeSH terms: Animals, Data Interpretation, Statistical, Humans, Computational Biology, Adaptive Immunity, High-Throughput Nucleotide Sequencing

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Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires

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