title: Molecular Methods and Bioinformatic Tools for Adjuvant Characterization by High-Throughput Sequencing.
abstract: Adjuvants in vaccine formulations are designed to enhance immune responses against a target antigen or pathogen. The ability of these vaccines to induce activation and differentiation of mature naïve B cells to produce pathogen-specific antibodies (immunoglobulins; Ig) helps guarantee long-lived humoral immunity. This process involves clonal expansion of antigen-specific B cells, genomic rearrangement of Ig heavy (IgH) and light (IgL) loci, somatic hypermutation (SHM), and clonal selection for affinity-matured antibody, resulting in a vast but directed repertoire of B cells expressing highly specific antibody proteins. High-throughput sequencing of the IgH and IgL complementary determining regions (CDRs) derived from various B cell populations provides an unprecedented way to observe dynamic responses of the humoral immune repertoire in response to vaccination. However, applying high-throughput sequencing (HTS) methodologies to multi-armed in vivo experiments requires careful coordination of sample preparation with downstream bioinformatics, particularly with regard to issues of quantitation, sequence fidelity, bar-coding, and multiplexing strategies. Here, we overview strategies of high-throughput sequencing and analysis of the adaptive immune complex loci applied to multi-armed, multiplexed experiments.
authors.affiliation: Imdaptive Inc., 3010 NW 56th Street, Seattle, WA, 98107, USA. steven.wiley@gmail.com.
authors.forename: Steven R
authors.initials: SR
authors.lastname: Wiley
authors.affiliation: Henry M. Jackson Foundation, Bethesda, MD, USA.
authors.forename: Vanitha S
authors.initials: VS
authors.lastname: Raman
mesh_terms: D000276:Adjuvants, Immunologic / Q000494:pharmacology*; D000818:Animals; D001402:B-Lymphocytes / Q000276:immunology*; D019295:Computational Biology / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007143:Immunoglobulin Heavy Chains / Q000235:genetics / Q000276:immunology; D007147:Immunoglobulin Light Chains / Q000235:genetics / Q000276:immunology; D051379:Mice; D014612:Vaccines / Q000494:pharmacology*
chemical_list: D000276:Adjuvants, Immunologic; D007143:Immunoglobulin Heavy Chains; D007147:Immunoglobulin Light Chains; D014612:Vaccines
keywords: Adaptive immune system; Adjuvant; Antibody; B cell; Bioinformatics; Complementarity determining region; High-throughput DNA sequencing; IgH; IgL; Immunoglobulin; Vaccine