Collection and storage of HLA NGS genotyping data for the 17th International HLA and Immunogenetics Workshop |
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| Authors: | Chia-Jung Chang Kazutoyo Osoegawa Robert P. Milius Martin Maiers Wenzhong Xiao Marcelo Fernandez-Viňa Steven J. Mack |
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| Affiliation: | 1. Stanford Genome Technology Center, Palo Alto, CA, USA;2. Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA;3. Bioinformatics Research, National Marrow Donor Program, Minneapolis, MN, USA;4. Massachusetts General Hospital and Shriners Hospital for Children, Boston, MA, USA;5. Department of Pathology, Stanford University Medical Center, Stanford, CA, USA;6. Center for Genetics, Children’s Hospital Oakland Research Institute, Oakland, CA, USA |
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| Abstract: | ![]()
For over 50?years, the International HLA and Immunogenetics Workshops (IHIW) have advanced the fields of histocompatibility and immunogenetics (H&I) via community sharing of technology, experience and reagents, and the establishment of ongoing collaborative projects. Held in the fall of 2017, the 17th IHIW focused on the application of next generation sequencing (NGS) technologies for clinical and research goals in the H&I fields. NGS technologies have the potential to allow dramatic insights and advances in these fields, but the scope and sheer quantity of data associated with NGS raise challenges for their analysis, collection, exchange and storage. The 17th IHIW adopted a centralized approach to these issues, and we developed the tools, services and systems to create an effective system for capturing and managing these NGS data. We worked with NGS platform and software developers to define a set of distinct but equivalent NGS typing reports that record NGS data in a uniform fashion. The 17th IHIW database applied our standards, tools and services to collect, validate and store those structured, multi-platform data in an automated fashion. We have created community resources to enable exploration of the vast store of curated sequence and allele-name data in the IPD-IMGT/HLA Database, with the goal of creating a long-term community resource that integrates these curated data with new NGS sequence and polymorphism data, for advanced analyses and applications. |
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| Keywords: | CSV Comma-Separated Values GFE Gene Feature Enumeration GL Genotype List HLA Human Leukocyte Antigen HML Histoimmunogenetics Markup Language H&I Histocompatibility and Immunogenetics IHIW International HLA and Immunogenetics Workshop IMGT ImMunoGeneTics IPD ImmunoPolymorphism Database IUPAC International Union of Pure and Applied Chemistry KIR Killer-cell Immunoglobulin-like Receptor MIRING Minimum Information for Reporting Immunogenomic NGS Genotyping NGS Next Generation Sequencing PI Principal Investigator RMAN Recovery Manager RSCA Reference Strand Conformation Analysis rSSO Reverse Sequence-Specific Oligo SBT Sequence-Based Typing sFTP secure File Transfer Protocol SS Sequence-Specific SSO Sequence-Specific Oligo SSP Sequence-Specific Priming WMDA World Marrow Donor Association WS Workshop XML eXtensible Markup Language International Workshop 17th IHIW Next generation sequencing HLA Database Data management XML HML |
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