Progress of the Biodefense Proteomics Research Centers

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Progress of the Biodefense Proteomics Research
Centers

• Joseph Breen, Ph.D.
• Project Officer, Proteomics Research Centers
• Genomics Program, Division of Microbiology and
  Infectious Diseases
• National Institute of Allergy Infectious
  Diseases
• National Institutes of Health
• Department of Health and Human Services
• May 30, 2007

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Outline

• Overview of Genomics Program
• Proteomics Research Centers and Progress
• Deliverables to the Community

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NIAID Genomic/Bioinformatic/Proteomic Program

• Resources and Reagents
• Genomic Capacity
• Basic and Applied Research Projects using Genomic
  Technologies

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Genome Sequence Data Microbial Seq. Centers

• Genomic/Proteomic Data Sets
• PFGRC
• Integrated Comparative Genomics
• SNPs/Biomarkers
• Gene Discovery Sets
• Comparative Protein Prof.
• Bioinformatics Res.Centers
• Microbial Gene/Pathway Annotation
• Computational Drug Disc. Pipeline
• Proteomics Research Centers
• Proteome-Targets and Structures
• Population Genetics Centers
• Host Biomarkers-Gene Sets

• Reagents
• PFGRC
• DNA Microarrays
• Protein Arrays
• Expression Clones
• Primer Sets
• PRCs
• Antibodies
• Strains
• DNA Microarray
• Clones

NIAID Microbial Genomic Tool Box Rapid Global
Access
Database/Bioinformatic Tools Bioinformatics
Resource Centers Pathogen Functional
Genomics Resource Center (PFGRC) Immune Epitope
Database PRC Administrative Resource Center (RC)

• Outreach
• Training
• Workshops
• Conferences

Technology Development Microbial Seq
Centers PFGRC Proteomic Resource Centers (PRCs)
For further info http//www.niaid.nih.gov/dmid/ge
nomes/
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Proteomics Research Centers

• The Mission
• Characterize the pathogen and/or host cell
  proteome
• Discover targets for potential candidates for the
  next generation of vaccines, therapeutics, and
  diagnostics
• Identify Protein Targets using
• Existing Technologies
• Augmenting Existing Technologies
• Creating Novel Proteomic Approaches
• Early Validation of Targets
• Bioinformatics and computational infrastructure
  for management and analysis of large amounts of
  proteomic data
• Informatics infrastructure includes tools
  necessary for transferring data, protocols and
  lists of available reagents to the Administrative
  Resource Center
• Generate data and make it publicly available

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Goal Provide Potential Targets and Reagents
to the Scientific Community
Potential Vaccine, Diagnostic and Therapeutic
Targets For the Scientific Community
Resource Center
Beginning to see critical mass of data that is
required for added value to the scientific
community
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PRC Output Available to the Scientific Community
Bottom Line Data output to the public is
increasing and the trend should continue
5/17/2007
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PRC-generated Reagents Available to the
Scientific Community
PRC Output by Data Type in Public Domain
8000
90
B.a. microarray B.a. clones S.t. strains T.g.
antisera Y2H clones SARS clones
V.c. clones
80
70
6000
60
50
Pathogen and Host Targets and
4000
Reagents
40
30
2000
20
10
0
0
closed bars
0-6
7-12
13-18
19-24
25-30
31-36
open bars
Time From Start of Contract (months)
Essential gene IDs
Antibodies
Synthetic peptides
protein IDs
Diff. Expd proteins
Gene expression
Clones
Protein IDs
3-D structures
Protein interactions
Immunopeptides
Bottom Line Reagents available to the public are
increasing and the trend should continue
5/17/2007
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Looking Forward

• Continue to complete deliverables and put them
  into the public domain
• Communication is key
• Identify challenges and work together for
  resolution
• Continue partnership between the Resource Center
  and PRCs for transfer of data/reagents/technologie
  s to the scientific community

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National Institute of Allergy and Infectious
Diseases (NIAID), NIH

• Administrative Resource Center
• Summary and Progress
• JoJo Stemple M.P.H.
• Project Officer for the Administrative Resource
  Center stemplek_at_niaid.nih.gov
• Genomics Program
• Division of Microbiology and Infectious Disease
  NIAID/NIH/DHHSMay 30, 2007

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Program précis

• The Administrative Resource Center (RC) serves as
  a central information source for reagents,
  validated protein targets and much more
• This information source is - a publicly
  accessible Web site designed, developed, and
  maintained by the RC containing data and
  technology protocols generated by each of the
  Proteomics Research Centers(PRCs)
  www.proteomicsresource.org.

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Communication
Scientific Working Group
Scientific Community
National Institute of Allergy and Infectious
Diseases
Proteomics Research Centers
Resource Center
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Program Goal

• The Admin Center will facilitate effective
  communication and collaboration among the PRCs,
  NIAID and the research community
• Administrative Resource for Biodefense Proteomic
  Centers will design, develop, and maintain a
  publicly accessible web site that contains data
  and technology protocols generated by each
  Proteomics Research Center. This database will
  serve as a central information source for
  reagents and validated protein targets. The web
  site for the Administrative Center is
  www.proteomicsresource.org.

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Integrated Data Resource

• Prime Contract 2 Sub-contracts 1 Resource
  Center
• The Partners
• Contract
• SSS- Social Scientific Systems
• Sub-contractors
• GU- Georgetown University
• VBI- Virginia Bioinformatic Institute
• The Center
• The Administrative Resource Center
• The Goal
• Drive data/reagents of value from the PRCs into
  the scientific community

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Challenges

• 3 centers with divergent expertise, logistics,
  defining tasks, integrating web efforts and
  communication.
• Working with 7 research centers that are all
  working with different pathogens/data types
• Conveying newly discovered information to the
  community in an informative, user friendly format
  that is useful to the public

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The Resource

• Title-
• Administrative Resource Center
• The Web site catalog is the Resource for the
  Scientific Community
• Catalog
• Master Protein Directory
• Master Reagent Directory
• Proteomics Data Center

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New and Improved
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Tracking as a Metric of Success
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Tracking
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Outreach to Scientific Community

• Web dissemination
• Reciprocal linking from
• PRC sites
• Meetings/Conferences
• Workshops
• Demonstrate mining
• capabilities
• Use of tools
• 1 page flyer- brochure
• Publications
• Other suggestions?

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Future Plans

• Further improvements on database
• Data transfer, loading, processing and deployment
• RC representatives will continue to participate
  in PRC calls
• Individual plan to work with each PRC

• SWG- Meet again in
• 6 months
• Development of SOPs will continue
• Assist in obtaining and depositing
  products/reagents
• Programmatic meeting

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Deliverables to the Public

• PRCs, in partnership with the RC have a main
  goal to
• Deposit the data/reagents of value from PRC
  research into the public domain

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Data Tracking System

• Tracking system implemented to ensure
  data/reagents are
• Flowing through the pipeline from PRC to RC
  and/or respective Repository
• Adhering to the deliverable timelines as
  described in progress reports
• Disseminated to the public in a timely manner

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Data/Reagent Flow
PRCs
Reagent NIAID approval
Data NIAID approval
Alert BEI, RC, cc NIAID (email reagent group)
Send reagent (email reagent group)
Yes (delete reminder)
No
Yes (delete reminder)
BEI/PFGRC receives
Yes (delete reminder)
Yes (delete reminder)
No
Available on Web site
RC PO - follow-up
NIAID- Spreadsheet entry and calendar reminder
PRC PO - follow-up
Clock starts AC -up to 1 month
NIAID- Spreadsheet entry and calendar reminder
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Data Plan Timeline
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Reagent Plan Timeline
5. PRC sends reagent to Repository by deadline
stated in reply email
1. Call with PRC requesting new data or reagents
3. PRC replies to Reagent Group including date
of reagent send
2. NIAID emails PRC with reagent submission
requirements
4. PRC PO approves or disapproves. NIAID enters
reagent tracking into NIAID master spreadsheet
6. Upon receipt of reagent- Repository emails
Reagent Group- including publicly available date
7. If reagents are not received PRC PO will
follow up with PRC
8. Reagent Group will be notified via email
when reagents are available at Repository
9. If reagents are not posted- RC PO will follow
up with Repository
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Data transfer tracking
Basic Research
Target Identification
Target /Reagent Transfer
Publicly Available Deliverable

Notifi- cation
Documen-tation
Documen-tation
Data
Documen-tation
From
To
Received
Publicly Available
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Reagent Repository

• BEI

An NIAID Contract awarded to American Type
Culture Collection Project Officers Ken
Cremer Susan Peacock BEI Operations Manager
Rebecca Bradford