年間 6 号発行
ISSN 印刷: 1040-8401
ISSN オンライン: 2162-6472
Indexed in
Identification of Antigen-Specific B-Cell Receptor Sequences from the Total B-Cell Repertoire
要約
Advances in next-generation sequencing now allow characterization of the global B-cell receptor (BCR) heavy-chain repertoire at a level that reflects its huge diversity. This technology has provided great insight into the structure of the BCR repertoire and how it responds to specific antigen stimuli. There are numerous potential clinical and research applications of BCR repertoire sequencing, but a major hurdle in the realization of these applications is the identification of the antigen-specific sequences of interest from within the total repertoire. To deconvolute the antigen-specific sequences from total repertoire, either a source of antigen-enriched sequence data is required with which to annotate the total repertoire, or de novo annotation methods must be used based on preconceptions of the features of antigen-specific sequences and their behavior following antigen-specific immune stimulation. We present a review of how these different methods can be applied to identify antigen-specific BCR sequences from the total BCR repertoire.
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Callan Curtis G., Mora Thierry, Walczak Aleksandra M., Repertoire sequencing and the statistical ensemble approach to adaptive immunity, Current Opinion in Systems Biology, 1, 2017. Crossref
-
Ghraichy Marie, Galson Jacob D., Kelly Dominic F., Trück Johannes, B-cell receptor repertoire sequencing in patients with primary immunodeficiency: a review, Immunology, 153, 2, 2018. Crossref
-
Khavrutskii Ilja V., Chaudhury Sidhartha, Stronsky Sabrina M., Lee Donald W., Benko Jacqueline G., Wallqvist Anders, Bavari Sina, Cooper Christopher L., Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses, Frontiers in Immunology, 8, 2017. Crossref
-
Reshetova Polina, van Schaik Barbera D. C., Klarenbeek Paul L., Doorenspleet Marieke E., Esveldt Rebecca E. E., Tak Paul-Peter, Guikema Jeroen E. J., de Vries Niek, van Kampen Antoine H. C., Computational Model Reveals Limited Correlation between Germinal Center B-Cell Subclone Abundancy and Affinity: Implications for Repertoire Sequencing, Frontiers in Immunology, 8, 2017. Crossref
-
Rajan Saravanan, Kierny Michael R., Mercer Andrew, Wu Jincheng, Tovchigrechko Andrey, Wu Herren, Dall′Acqua William F., Xiao Xiaodong, Chowdhury Partha S., Recombinant human B cell repertoires enable screening for rare, specific, and natively paired antibodies, Communications Biology, 1, 1, 2018. Crossref
-
Olson Branden J., Matsen Frederick A., The Bayesian optimist's guide to adaptive immune receptor repertoire analysis, Immunological Reviews, 284, 1, 2018. Crossref
-
Fowler Anna, Galson Jacob D., Trück Johannes, Kelly Dominic F., Lunter Gerton, Inferring B cell specificity for vaccines using a Bayesian mixture model, BMC Genomics, 21, 1, 2020. Crossref
-
Ralph Duncan K., Matsen Frederick A., Wallqvist Anders, Using B cell receptor lineage structures to predict affinity, PLOS Computational Biology, 16, 11, 2020. Crossref
-
Ripoll Daniel R., Chaudhury Sidhartha, Wallqvist Anders, Deane Charlotte M., Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification, PLOS Computational Biology, 17, 3, 2021. Crossref
-
Trück Johannes, Eugster Anne, Barennes Pierre, Tipton Christopher M, Luning Prak Eline T, Bagnara Davide, Soto Cinque, Sherkow Jacob S, Payne Aimee S, Lefranc Marie-Paule, Farmer Andrew, Bostick Magnolia, Mariotti-Ferrandiz Encarnita, Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling, eLife, 10, 2021. Crossref
-
Eugster Anne, Bostick Magnolia L., Gupta Nidhi, Mariotti-Ferrandiz Encarnita, Kraus Gloria, Meng Wenzhao, Soto Cinque, Trück Johannes, Stervbo Ulrik, Luning Prak Eline T., AIRR Community Guide to Planning and Performing AIRR-Seq Experiments, in Immunogenetics, 2453, 2022. Crossref
-
Greiff Victor, Menzel Ulrike, Miho Enkelejda, Weber Cédric, Riedel René, Cook Skylar, Valai Atijeh, Lopes Telma, Radbruch Andreas, Winkler Thomas H., Reddy Sai T., Systems Analysis Reveals High Genetic and Antigen-Driven Predetermination of Antibody Repertoires throughout B Cell Development, Cell Reports, 19, 7, 2017. Crossref