Introduction

In vitro selection has been an essential tool in the development of recombinant antibodies against various antigen targets. Deep sequencing has recently been gaining ground as an alternative and valuable method to analyze such antibody selections. The analysis provides a novel and extremely detailed view of selected antibody populations, and allows the identification of specific antibodies using only sequencing data, potentially eliminating the need for expensive and laborious low-throughput screening methods such as enzyme-linked immunosorbant assay. The high cost and the need for bioinformatics experts and powerful computer clusters, however, have limited the general use of deep sequencing in antibody selections. Here, we describe the AbMining ToolBox, an open source software package for the straightforward analysis of antibody libraries sequenced by the three main next generation sequencing platforms (454, Ion Torrent, MiSeq). The ToolBox is able to identify heavy chain CDR3s as effectively as more computationally intense software, and can be easily adapted to analyze other portions of antibody variable genes, as well as the selection outputs of libraries based on different scaffolds. The software runs on all common operating systems (Microsoft Windows, Mac OS X, Linux), on standard personal computers, and sequence analysis of 1-2 million reads can be accomplished in 10-15 min, a fraction of the time of competing software. Use of the ToolBox will allow the average researcher to incorporate deep sequence analysis into routine selections from antibody display libraries.

Publications

  1. The antibody mining toolbox: an open source tool for the rapid analysis of antibody repertoires.
    Cite this
    D'Angelo S, Glanville J, Ferrara F, Naranjo L, Gleasner CD, Shen X, Bradbury AR, Kiss C, 2014-01-01 - mAbs

Credits

  1. Sara D'Angelo
    Developer

    New Mexico Consortium; Los Alamos, NM, United States of America

  2. Jacob Glanville
    Developer

  3. Fortunato Ferrara
    Developer

    New Mexico Consortium; Los Alamos, NM, United States of America

  4. Leslie Naranjo
    Developer

  5. Cheryl D Gleasner
    Developer

  6. Xiaohong Shen
    Developer

  7. Andrew R M Bradbury
    Developer

  8. Csaba Kiss
    Investigator

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Summary
AccessionBT000030
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByCsaba Kiss