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Pathogenomics
How this project began:
Ann Rose - take advantage of DNA sequence information - genomics
Julian Davies - use the information to understand and control infectious disease, pathogenicity
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Pathogenomics
Goal:
Identify previously unrecognized mechanisms of infectious disease.
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Pathogenomics
Getting started, the PWIAS funded workshop:
December, 1997
We invited major genome scientists sequencing and analyzing data from bacterial genomes, and
Company researchers using sequence information to identify potential drug targets
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Recruitment of Key Bioinformaticists
Steven J. Jones
Sanger Centre (UK)
to
BC Genome Sequence
Centre, BC Cancer Agency
B. Francis OuelletteNational Centre for
Biotechnology
Information, NIH (USA)to
Centre for
Molecular Medicine
and Therapeutics, UBC
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Pathogenomics
A unique opportunity:
Take an informatics approach
Identify ‘candidates’
Functionally test in both the pathogen and host
Within an evolutionary perspective
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Post-funding New members
- NSERC student,
Audrey de Koenig with Sally Otto
- New Faculty member,
Patrick Keeling
- Recently appointed Director CDC,
Bob Brunham
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Informatics/Bioinformatics• BC Genome Sequence Centre
• Centre for Molecular Medicine and Therapeutics
Pathogen Functions• Dept. Microbiology
• Biotechnology Laboratory
• Dept. Medicine
• BC Centre for Disease Control
Host Functions• Dept. Medical Genetics
• C. elegans Reverse Genetics Facility
• Dept. Biological Sciences SFU
Interdisciplinary group
Evolutionary Theory• Dept of Zoology
• Dept of Botany
• Canadian Institute for Advanced Research
Coordinator
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Pathogenomics
How does it work:
Very well !
Monthly meetings
Steve’s program
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Screen for candidate genes.Search pathogen genes against sequence databases. Identify those with notable similarity to eukaryotic genes.
Rank candidates.- how much like host protein?- info available about protein?
Prioritize for further biological study. - Previously studied biologically? - Can UBC microbiologists study it? - C. elegans homolog?
Evolutionary significance. - Horizontal transfer? Date of transfer? Coevolution? Similar by chance?
Modify screening method /algorithm
Approach
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• Sequence comparisons are automated & continually updated
• Interdisciplinary team examine the pathogen gene and similar host gene
• Insight gained into horizontal gene transfer events
• The evolution of pathogen-host interactions.
Power of the Approach
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Pathogenomics Group Reference Website
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Presentations
• Medical Genetics Research Day
– November 12, 1999
– Talk: “Pathogenomics”
– Poster: “Pathogenomics: An Interdisciplinary Approach for the Study of Infectious Disease”
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Presentations, this week
• Canadian Bioinformatics workshops, at Harbour View Centre
• Pathogenomics is there!– Three of our members
participating– Pathogenomics Poster
presented
Genomics
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Upcoming Presentations
• HUGO/HGM2000 meeting– April 9-12, 2000, Vancouver,
Canada
• Genomes 2000 conference– April 11-15, 2000, Paris, France
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Pathogenomics Contributions
- Generation of computer software - Creation of a public database
- Publication of results in research journals, and
by means of a web site
- Promote research collaboration
- Contribute to the profile of UBC and PWIAS
- Discover new mechanisms of infection, and
- Gain insights that will improve human health