Informatics of Genomic Data Component: Update
The advent of genome-wide SNP typing and NGS genotyping methods heralds new insights and innovations for the fields of histocompatibility, immunogenetics and immunogenomics. However, the scope of the “big-data” generated using these technologies presents new challenges for their management, exchange, integration and application. The Informatics of Genomic Data component of the 17th Workshop has been established to assess and address these challenges, with the overall goal of identifying data-related “best-practices” and standards for maximizing the utility of these new methods. The leaders of this component are Steven J. Mack, Jill A. Hollenbach, Martin Maiers, and Paul J. Norman.
The Informatics of Genomic Data component includes the Informatics Core as well as a series of Informatics Projects. The Informatics Core is a central facility for the collection, storage, exchange and analysis of all workshop data and data-analysis results. Initial Quality Control (QC) evaluations, for the enrollment of experimental-data-generating laboratories, and periodic Quality Assurance (QA) evaluations will also be stored and scored in the Informatics Core.
The web-portal for the Informatics Core can be found at http://workshop.17ihiw.org. Using this portal, investigators can register for the 17th Workshop, enroll members of their laboratories and research teams, enroll in components and projects, upload sample demographic data, pedigrees, typing results and typing meta-data, and apply for data access privileges. Raw NGS read data can be submitted to the Informatics Core via the exchange of physical hard drives, or via an SFTP portal that will be opened later this year.
Where possible, the Informatics Core will support centralized data-analyses for projects in in all workshop components; these functions will be activated over the course of 2016. While some analyses may be performed outside of the Informatics Core, the results of those analyses will be stored in the Informatics Core as well.
Informatics Projects are specific to the Informatics of Genomic Data component; these projects pertain to the maximization of the utility of immunogenomic data generated via NGS methods for the study of histocompatibility and immunogenetics. Investigators are welcome and invited to propose Informatics Projects on the management, exchange and meta-analysis of histocompatibility, immunogenetic and immunogenomic data, as well as Informatics Projects related to the development of community standards and reporting guidelines for these data. Investigator participation in current Informatics Projects (see below) is also welcome.
Current Informatics Projects include:
Analysis of NGS Typing Data
The focus of this project is the development and application of methods and resources for the analysis of HLA and KIR consensus sequences and genotypes generated via NGS methods for research (e.g. disease association, population genetics) and clinical applications.
Common, Well-Documented and Rare HLA Alleles
The focus of this project is to extend the knowledge of HLA allele prevalence, and harmonize the Common and Well Documented HLA alleles catalogue and Allele Frequencies Net Database’s Rare Alleles Project by investigating the distribution of HLA alleles.
Meta-Analytic Comparison of NGS Methods
The focus of this project is to compare outputs from the available NGS genotyping softwares, including:
- consensus sequences generated from NGS reads,
- genotypes generated from consensus sequences, and
- evaluating equivalence of genotyping results between NGS platforms/methods.
Standards for Exchange of NGS Genotyping
The focus of this project is to develop and evaluate approaches for recording, sharing and using NGS genotype data.
We look forward to your participation in the 17th Workshop’s Informatics of Genomic Data component. News and updates on the Informatics of Genomic Data component will appear on the 17th Workshop website at http://17ihiw.org/core-workshop-functions/informatics-of-genomic-data.