Centers of Excellence for Influenza Research and Surveillance6th Annual Meeting

Aug 1, 2012

Status of IRD Development

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

Current CEIRS Data in IRD

CEIRS Surveillance Samples

2008 2009 2010 2011 2012 Total0

50,000

100,000

150,000

200,000

250,000

300,000

350,000

CEIRS Surveillance Samples

# of

sam

ples

94% avian5.8% non-human mam.0.2% human

Surveillance Sample Stats

Avian Records Avian %

Non-Human Mammalian

Records Mammalian %

Total 197,207 14,098

Tested 175,746 89% 12,973 92%

Flu-positive 10,136 5.8% 510 3.9%

Linked to sequence 772 7.6% 11 2.2%

*as of May 1, 2012

Serology Samples

Species category Submission Year Sample CountAvian 2011 254

Avian 2012 962

Human 2012 201

Non Human Mammalian 2010 200

Non Human Mammalian 2011 986

Non Human Mammalian 2012 72

TOTAL 2675

Influenza Serology Data

CEIRS Immunology Data in IRD

CEIRS Immunology Data in IRD

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

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

IRD Enhancements Over Past Year

Sequence Search Page Enhancements

Quick Text Search

Surveillance Data from Map

Spinning 3D Protein Structure Movie

Phylogenetic Tree DecorationDecorate by:

– Host species• Avian: Avian

grouped/separated– Country– Year– HA subtype– NA subtype– HA & NA subtype– Geographic region– Flu season– SFVT

Manual decoration

Metadata-driven Comparative Analysis Tool

Sequence Feature Variant Type (SFVT)

Sequence Feature Submission Tool

DMID Systems Biology Program

Host Factor Data

IRD/ViPR Publications 2012

Future Development Plans

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

Search

• Query Capabilities– Ability to search for high-path and/or low-path

strains (using sequence biomarkers)

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

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.)

Surveillance

• Identify NIAID-funded human surveillance studies and solicit deposition into IRD

• Develop additional use-cases to identify additional helpful data types

Immunology

• Epitopes– Add search options such as: CD4, CD8, host

• Serology– Solicit feedback from community on use-cases– Identify volunteers for data submission

PA-X Prediction for All Strains

• Build on analysis performed earlier this year by Jagger et 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

H5 clade annotation tool

• Automated clade determination for any query HA sequence

• Match WHO clade definitions

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