Abstract
Aim The 17th International HLA and Immunogenetics Workshops (IHIW) focuses on the application of next generation sequencing (NGS) technologies for histocompatibility and immunogenomic clinical and research goals. However, the scope and sheer quantity of NGS data raises challenges for their analysis, collection, exchange and storage. The 17th IHIW has adopted a centralized approach to these issues, with the goals of developing tools, services and systems to capture and manage these NGS data, and leveraging the vast store of sequence and allele data in the IPD-IMGT/HLA Database. Methods We worked with NGS platform and software developers to define NGS typing reports that record NGS data in a uniform fashion. The IHIW database and data-storage facility houses typing reports, FASTQ files, subject and specimen data, and pedigrees, and manages the accounts and data-access privileges for 17th IHIW participants. IHIW database tools and services are scripted in the Perl, R or Python languages. Results We defined three distinct typing report formats [Histoimmunogenetics Markup Language (HML), IHIW eXtensible Markup Language (XML), and GenDx XML formats] that record HLA genotyping data and meta-data in equivalent fashion. Our tools convert HML and GenDx XML to IHIW XML, automate and streamline the submission of IHIW XML reports, validate each typing report upon submission, and automate the standardized reporting of novel polymorphisms. All 17th IHIW HLA data are standardized to IPD-IMGT/HLA Database version 3.25.0, with genotype data generated under other database versions converted to 3.25.0. Conclusions The 17th IHIW database applies our standards, tools and services to consume, validate and store structured NGS HLA data generated by GenDx, Illumina, Immucor, Omixon and One Lambda in an automated fashion. The HLA genotyping data and meta-data in these typing reports are validated and standardized for use in 17th IHIW projects, and the database itself will be available for future workshops.
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