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

Pathogenomics

Goal:

Identify previously unrecognized mechanisms of infectious disease.

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

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

Pathogenomics

A unique opportunity:

Take an informatics approach

Identify ‘candidates’

Functionally test in both the pathogen and host

Within an evolutionary perspective

Post-funding New members

- NSERC student,

Audrey de Koenig with Sally Otto

- New Faculty member,

Patrick Keeling

- Recently appointed Director CDC,

Bob Brunham

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

Pathogenomics

How does it work:

Very well !

Monthly meetings

Steve’s program

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

• 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

Pathogenomics Group Reference Website

Presentations

• Medical Genetics Research Day

– November 12, 1999

– Talk: “Pathogenomics”

– Poster: “Pathogenomics: An Interdisciplinary Approach for the Study of Infectious Disease”

Presentations, this week

• Canadian Bioinformatics workshops, at Harbour View Centre

• Pathogenomics is there!– Three of our members

participating– Pathogenomics Poster

presented

Genomics

Upcoming Presentations

• HUGO/HGM2000 meeting– April 9-12, 2000, Vancouver,

Canada

• Genomes 2000 conference– April 11-15, 2000, Paris, France

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