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| Content Provider | Springer Nature : BioMed Central |
|---|---|
| Author | Moorhouse, Michael J van Zessen, David IJspeert, Hanna Hiltemann, Saskia Horsman, Sebastian van der Spek, Peter J van der Burg, Mirjam Stubbs, Andrew P |
| 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. |
| Related Links | https://bmcimmunol.biomedcentral.com/counter/pdf/10.1186/s12865-014-0059-7.pdf |
| Ending Page | 9 |
| Page Count | 9 |
| Starting Page | 1 |
| File Format | HTM / HTML |
| ISSN | 14712172 |
| DOI | 10.1186/s12865-014-0059-7 |
| Journal | BMC Immunology |
| Issue Number | 1 |
| Volume Number | 15 |
| Language | English |
| Publisher | BioMed Central |
| Publisher Date | 2014-12-13 |
| Access Restriction | Open |
| Subject Keyword | Immunology Allergology Vaccine Cytokines and Growth Factors Next generation sequencing Immunoglobulin heavy chain Repertoire IMGT/HIGHV-QUEST igBLAST |
| Content Type | Text |
| Resource Type | Article |
| Subject | Immunology |
| Journal Impact Factor | 2.9/2023 |
| 5-Year Journal Impact Factor | 3.3/2023 |
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