title: ImmunoGlobulin galaxy (IGGalaxy) for simple determination and quantitation of immunoglobulin heavy chain rearrangements from NGS.
abstract: BACKGROUND
  Sequence analysis of immunoglobulin heavy chain (IGH) gene rearrangements and frequency analysis is a powerful tool for studying the immune repertoire, immune responses and immune dysregulation in health and disease. The challenge is to provide user friendly, secure and reproducible analytical services that are available for both small and large laboratories which are determining VDJ repertoire using NGS technology.
  
  
  RESULTS
  In this study we describe ImmunoGlobulin Galaxy (IGGalaxy)- a convenient web based application for analyzing next-generation sequencing results and reporting IGH gene rearrangements for both repertoire and clonality studies. IGGalaxy has two analysis options one using the built in igBLAST algorithm and the second using output from IMGT; in either case repertoire summaries for the B-cell populations tested are available. IGGalaxy supports multi-sample and multi-replicate input analysis for both igBLAST and IMGT/HIGHV-QUEST. We demonstrate the technical validity of this platform using a standard dataset, S22, used for benchmarking the performance of antibody alignment utilities with a 99.9 % concordance with previous results. Re-analysis of NGS data from our samples of RAG-deficient patients demonstrated the validity and user friendliness of this tool.
  
  
  CONCLUSIONS
  IGGalaxy provides clinical researchers with detailed insight into the repertoire of the B-cell population per individual sequenced and between control and pathogenic genomes. IGGalaxy was developed for 454 NGS results but is capable of analyzing alternative NGS data (e.g. Illumina, Ion Torrent). We demonstrate the use of a Galaxy virtual machine to determine the VDJ repertoire for reference data and from B-cells taken from immune deficient patients. IGGalaxy is available as a VM for download and use on a desktop PC or on a server.
authors.affiliation: Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands. michael.moorhouse@oicr.on.ca.|Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada. michael.moorhouse@oicr.on.ca.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Moorhouse
authors.affiliation: Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands. d.vanzessen@erasmusmc.nl.|Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, The Netherlands. d.vanzessen@erasmusmc.nl.
authors.forename: David
authors.initials: D
authors.lastname: van Zessen
authors.affiliation: Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands. h.ijspeert@erasmusmc.nl.
authors.forename: Hanna
authors.initials: H
authors.lastname: IJspeert
authors.affiliation: Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, The Netherlands. s.hiltemann@erasmusmc.nl.|Department of Experimental Urology, Erasmus MC, Erasmus University Medical Center, s-Gravendijkwal 230, 3015, CE, Rotterdam, The Netherlands. s.hiltemann@erasmusmc.nl.
authors.forename: Saskia
authors.initials: S
authors.lastname: Hiltemann
authors.affiliation: Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, The Netherlands. s.horsman@erasmusmc.nl.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Horsman
authors.affiliation: Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, The Netherlands. p.vanderspek@erasmusmc.nl.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: van der Spek
authors.affiliation: Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands. m.vanderburg@erasmusmc.nl.
authors.forename: Mirjam
authors.initials: M
authors.lastname: van der Burg
authors.affiliation: Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, The Netherlands. a.stubbs@erasmusmc.nl.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Stubbs
mesh_terms: D030561:Databases, Nucleic Acid; D015326:Gene Rearrangement, B-Lymphocyte, Heavy Chain; D006801:Humans; D007153:Immunologic Deficiency Syndromes / Q000235:genetics* / Q000276:immunology; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software