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CSReport: A New Computational Tool Designed for Automatic Analysis of Class Switch Recombination Junctions Sequenced by High-Throughput Sequencing.
Boyer, François; Boutouil, Hend; Dalloul, Iman; Dalloul, Zeinab; Cook-Moreau, Jeanne; Aldigier, Jean-Claude; Carrion, Claire; Herve, Bastien; Scaon, Erwan; Cogné, Michel; Péron, Sophie.
Afiliación
  • Boyer F; Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.
  • Boutouil H; CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.
  • Dalloul I; Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.
  • Dalloul Z; CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.
  • Cook-Moreau J; Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.
  • Aldigier JC; CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.
  • Carrion C; Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.
  • Herve B; CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.
  • Scaon E; Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.
  • Cogné M; CNRS, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.
  • Péron S; Université de Limoges, Contrôle de la Réponse Immune B et Lymphoproliférations, UMR 7276, F-87000 Limoges, France.
J Immunol ; 198(10): 4148-4155, 2017 05 15.
Article en En | MEDLINE | ID: mdl-28416601
ABSTRACT
B cells ensure humoral immune responses due to the production of Ag-specific memory B cells and Ab-secreting plasma cells. In secondary lymphoid organs, Ag-driven B cell activation induces terminal maturation and Ig isotype class switch (class switch recombination [CSR]). CSR creates a virtually unique IgH locus in every B cell clone by intrachromosomal recombination between two switch (S) regions upstream of each C region gene. Amount and structural features of CSR junctions reveal valuable information about the CSR mechanism, and analysis of CSR junctions is useful in basic and clinical research studies of B cell functions. To provide an automated tool able to analyze large data sets of CSR junction sequences produced by high-throughput sequencing (HTS), we designed CSReport, a software program dedicated to support analysis of CSR recombination junctions sequenced with a HTS-based protocol (Ion Torrent technology). CSReport was assessed using simulated data sets of CSR junctions and then used for analysis of Sµ-Sα and Sµ-Sγ1 junctions from CH12F3 cells and primary murine B cells, respectively. CSReport identifies junction segment breakpoints on reference sequences and junction structure (blunt-ended junctions or junctions with insertions or microhomology). Besides the ability to analyze unprecedentedly large libraries of junction sequences, CSReport will provide a unified framework for CSR junction studies. Our results show that CSReport is an accurate tool for analysis of sequences from our HTS-based protocol for CSR junctions, thereby facilitating and accelerating their study.
Asunto(s)

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Recombinación Genética / Programas Informáticos / Cambio de Clase de Inmunoglobulina / Secuenciación de Nucleótidos de Alto Rendimiento Tipo de estudio: Guideline Idioma: En Revista: J Immunol Año: 2017 Tipo del documento: Article País de afiliación: Francia

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Recombinación Genética / Programas Informáticos / Cambio de Clase de Inmunoglobulina / Secuenciación de Nucleótidos de Alto Rendimiento Tipo de estudio: Guideline Idioma: En Revista: J Immunol Año: 2017 Tipo del documento: Article País de afiliación: Francia