A rapid visualization pipeline for the 2009 A/H1N1 influenza pandemic Donovan Parks Norm MacDonald Rob Beiko.

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Presentation transcript:

A rapid visualization pipeline for the 2009 A/H1N1 influenza pandemic Donovan Parks Norm MacDonald Rob Beiko

A little biology Motivation Data acquisition pipeline GenGIS: a genomic GIS framework ExamplesOutline1/10 Photo obtained from commons.wikimedia.org

H1N1 Biology 2/10 Modified photo from commons.wikimedia.org

Motivation3/10 Move from reactive to preventive health strategy Increased sampling requires automated tools PandemicYearDeaths worldwide (est.) Fatality rate Spanish flu to 100 million> 2.5% Asian flu million< 0.1% Hong Kong flu million< 0.1% Seasonal fluEvery year million< 0.1%

Pipeline Overview 4/10

Data Acquisition Pipeline 5/10

SeqMonitor6/10

GenGIS: A Genomic GIS Framework 7/10

Global Genetic Diversity of NA 8/10

NA Polymorphism 9/10 October 19, 2009

Conclusions Global, continuous sequencing of infectious diseases would allows us to implement preventive health strategies. Automated tools will be necessary to provide analyses to inform such policies. 10/10

Further Information SeqMonitor: – MacDonald, N. J., Parks, D. H., and Beiko, R. G. SeqMonitor: Influenza Analysis Pipeline and Visualization. PLoS Currents: Influenza. 23 September 2009: RRN1040. GenGIS: – Parks, D. H., Porter, M., Churcher, S., Wang, S., Blouin, C., Whalley, J., Brooks, S., and Beiko, R. G. GenGIS: A geospatial information system for genomic data. Genome Res. July 27, – Parks, D. H., MacDonald, N. J., and Beiko, R. G. Tracking the evolution and geographic spread of inﬂuenza A. PLoS Currents: Inﬂuenza. 21 August 2009: RRN1014.