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Centers of Excellence for Influenza Research and Surveillance 6 th Annual Meeting Aug 1, 2012

This annual meeting will discuss current data, surveillance, serology, immunology, and enhancements in the IRD. Topics include search improvements, 3D movies, phylogenetic tree decoration, comparative genomics analysis, and future development plans.

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Centers of Excellence for Influenza Research and Surveillance 6 th Annual Meeting Aug 1, 2012

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  1. Status of IRD Development Centers of Excellence for Influenza Research and Surveillance 6th Annual Meeting Aug 1, 2012

  2. Session Topics • Current CEIRS data in IRD • Surveillance • Serology • Immunology & ImmPort • IRD enhancements over past year • Search improvements • Surveillance data from map • Support for serology data • 3D movies • Phylogenetic tree decoration • Metadata-driven comparative genomics analysis • Sequence feature submission tool • Host factor data • Publications • Plans for future development

  3. Current CEIRS Data in IRD

  4. CEIRS Surveillance Samples 94% avian 5.8% non-human mam. 0.2% human

  5. Surveillance Sample Stats *as of May 1, 2012

  6. Serology Samples

  7. Influenza Serology Data

  8. CEIRS Immunology Data in IRD

  9. CEIRS Immunology Data in IRD

  10. Introduction to ImmPort • Immunology Database and Analysis Portal (ImmPort) • Bioinformatics Integration Support Contract (BISC) • Purpose • Warehouse for storing immunology experiment data • Integrate data with analysis and visualization tools • Provide access to research community • Projects • Population Genetics Analysis Program • HLA Region Genetics in Immune-mediated Diseases • Modeling Immunity for Biodefense • Others

  11. Additional ImmPort Capabilities • Integrate data from multiple resources • OMIM, GO, synonyms, protein-protein interactions, etc. • Suite of data analysis and visualization tools • Microarray • Flow Cytometry • Other “-omics” platforms

  12. IRD Enhancements Over Past Year

  13. Sequence Search Page Enhancements

  14. Quick Text Search

  15. Surveillance Data from Map

  16. Spinning 3D Protein Structure Movie

  17. Phylogenetic Tree Decoration Decorate by: • Host species • Avian: Avian grouped/separated • Country • Year • HA subtype • NA subtype • HA & NA subtype • Geographic region • Flu season • SFVT Manual decoration

  18. Metadata-driven Comparative Analysis Tool

  19. Sequence Feature Variant Type (SFVT)

  20. Sequence Feature Submission Tool

  21. DMID Systems Biology Program

  22. Host Factor Data

  23. IRD/ViPR Publications 2012

  24. Future Development Plans

  25. User Support and Outreach • Data • Evaluate feasibility of supporting Antigenic Cartography • Prepare packages of (correctly-formatted) data to export to external tools • Outreach • Perform on-site outreach at CEIRS centers • Continue developing tutorials for existing tools & features

  26. Search • Query Capabilities • Ability to search for high-path and/or low-path strains (using sequence biomarkers)

  27. Comparative Genomics • Develop PCR Primer design tool (exclude orthologs) • Increase SF definitions for: virulence, host specificity, replication, etc. • Provide a new tool to assign (or convert between) sequence coordinate schemes

  28. Annotation and Host Factor Data • Ensure sequence submissions are appropriately prepared (i.e. no primer sequence, etc.) • Increase number of host factor datasets • Develop method to handle different statistical methods from various “-omics” platforms (e.g. microarray, proteomics, etc.)

  29. Surveillance • Identify NIAID-funded human surveillance studies and solicit deposition into IRD • Develop additional use-cases to identify additional helpful data types

  30. Immunology • Epitopes • Add search options such as: CD4, CD8, host • Serology • Solicit feedback from community on use-cases • Identify volunteers for data submission

  31. PA-X Prediction for All Strains • Build on analysis performed earlier this year by Jaggeret al.Science 2012 Jul 13;337(6091):199-204 • Identified new protein on segment 3 using ~1000 sequences • Frameshift occurs at codon 190 in PA protein, results in new C-terminus • IRD will extend this analysis across all segment 3’s in resource • Add PA-X annotation to existing IRD sequence records • Allow users to search for PA-X protein sequences • Provide data that can assist in downstream comparative genomics analyses

  32. H5 clade annotation tool • Automated clade determination for any query HA sequence • Match WHO clade definitions

  33. NGS Deep Sequencing Data • Primary data in SRA • Derived data in IRD • Positions with sequence variation • Proportion of read with a particular sequence variation • Metadata to understand the context

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