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MAbs. 2015;7(3):516-24. doi: 10.1080/19420862.2015.1026502.

Reconstructing and mining the B cell repertoire with ImmunediveRsity.

Author information

1
a Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública (CISEI-INSP); Cuernavaca , Morelos , México.

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/.

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

PMID:
25875140
PMCID:
PMC4622655
DOI:
10.1080/19420862.2015.1026502
[Indexed for MEDLINE]
Free PMC Article

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