title: Reconstructing and mining the B cell repertoire with ImmunediveRsity.
abstract: The B cell antigen receptor repertoire is highly diverse and constantly modified by clonal selection. High-throughput DNA sequencing (HTS) of the lymphocyte repertoire (Rep-Seq) represents a promising technology to explore such diversity ex-vivo and assist in the identification of antigen-specific antibodies based on molecular signatures of clonal selection. Therefore, integrative tools for repertoire reconstruction and analysis from antibody sequences are needed. We developed ImmunediveRity, a stand-alone pipeline primarily based in R programming for the integral analysis of B cell repertoire data generated by HTS. The pipeline integrates GNU software and in house scripts to perform quality filtering, sequencing noise correction and repertoire reconstruction based on V, D and J segment assignment, clonal origin and unique heavy chain identification. Post-analysis scripts generate a wealth of repertoire metrics that in conjunction with a rich graphical output facilitates sample comparison and repertoire mining. Its performance was tested with raw and curated human and mouse 454-Roche sequencing benchmarks providing good approximations of repertoire structure. Furthermore, ImmunediveRsity was used to mine the B cell repertoire of immunized mice with a model antigen, allowing the identification of previously validated antigen-specific antibodies, and revealing different and unexpected clonal diversity patterns in the post-immunization IgM and IgG compartments. Although ImmunediveRsity is similar to other recently developed tools, it offers significant advantages that facilitate repertoire analysis and repertoire mining. ImmunediveRsity is open source and free for academic purposes and it runs on 64 bit GNU/Linux and MacOS. Available at: https://bitbucket.org/ImmunediveRsity/immunediversity/.
authors: a Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública (CISEI-INSP); Cuernavaca , Morelos , México.
authors: Bernardo
authors: B
authors: Cortina-Ceballos
authors: Elizabeth Ernestina
authors: EE
authors: Godoy-Lozano
authors: Hugo
authors: H
authors: Sámano-Sánchez
authors: Andrés
authors: A
authors: Aguilar-Salgado
authors: Martín Del Castillo
authors: Mdel C
authors: Velasco-Herrera
authors: Carlos
authors: C
authors: Vargas-Chávez
authors: Daniel
authors: D
authors: Velázquez-Ramírez
authors: Guillermo
authors: G
authors: Romero
authors: José
authors: J
authors: Moreno
authors: Juan
authors: J
authors: Téllez-Sosa
authors: Jesús
authors: J
authors: Martínez-Barnetche
mesh_terms: D000818:Animals; D000911:Antibodies, Monoclonal / Q000235:genetics* / Q000276:immunology; D000918:Antibody Specificity / Q000235:genetics*; D006801:Humans; D007074:Immunoglobulin G / Q000235:genetics / Q000276:immunology; D007075:Immunoglobulin M / Q000235:genetics / Q000276:immunology; D051379:Mice; D011947:Receptors, Antigen, B-Cell / Q000235:genetics* / Q000276:immunology; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D000911:Antibodies, Monoclonal; D007074:Immunoglobulin G; D007075:Immunoglobulin M; D011947:Receptors, Antigen, B-Cell
keywords: CDR3; CDRH3, heavy chain complementarity determining region 3; HEL, hen egg lysozyme; Ig repertoire; Rep-Seq, repertoire sequencing; SHM, somatic hypermutation.; data mining; high-throughput sequencing