title: The antibody mining toolbox: an open source tool for the rapid analysis of antibody repertoires.
abstract: 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.
authors.affiliation: New Mexico Consortium; Los Alamos, NM, USA.
authors.forename: Sara
authors.initials: S
authors.lastname: D'Angelo
authors.affiliation: Stanford Immunology; Stanford University; Stanford, CA USA.
authors.forename: Jacob
authors.initials: J
authors.lastname: Glanville
authors.affiliation: New Mexico Consortium; Los Alamos, NM, USA.
authors.forename: Fortunato
authors.initials: F
authors.lastname: Ferrara
authors.affiliation: B Division; Los Alamos National Laboratory; Los Alamos, NM USA.
authors.forename: Leslie
authors.initials: L
authors.lastname: Naranjo
authors.affiliation: B Division; Los Alamos National Laboratory; Los Alamos, NM USA.
authors.forename: Cheryl D
authors.initials: CD
authors.lastname: Gleasner
authors.affiliation: B Division; Los Alamos National Laboratory; Los Alamos, NM USA.
authors.forename: Xiaohong
authors.initials: X
authors.lastname: Shen
authors.affiliation: B Division; Los Alamos National Laboratory; Los Alamos, NM USA.
authors.forename: Andrew R M
authors.initials: AR
authors.lastname: Bradbury
authors.affiliation: B Division; Los Alamos National Laboratory; Los Alamos, NM USA.
authors.forename: Csaba
authors.initials: C
authors.lastname: Kiss
mesh_terms: D022801:Complementarity Determining Regions / Q000235:genetics* / Q000276:immunology; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*; D057127:Single-Chain Antibodies / Q000235:genetics* / Q000276:immunology; D012984:Software
chemical_list: D022801:Complementarity Determining Regions; D057127:Single-Chain Antibodies
keywords: AbMining ToolBox; HCDR3; antibody library; deep sequencing; regular expression