Bio-banking and Metagenomics Platforms for Pathogen DiscoveryGeorge Michuki, Absolomon Kihara, Alan Orth, Cecilia Rumberia...
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Bio-banking and metagenomics platforms for pathogen discovery

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Poster by George Michuki, Absolomon Kihara, Alan Orth, Cecilia Rumberia and Steve Kemp presented at the Sequencing, Finishing and Analysis in the Future (SFAF) meeting held at Santa Fe, New Mexico, 29-31 May 2013.

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Bio-banking and metagenomics platforms for pathogen discovery

  1. 1. Bio-banking and Metagenomics Platforms for Pathogen DiscoveryGeorge Michuki, Absolomon Kihara, Alan Orth, Cecilia Rumberia and Steve KempIntroductionThere has been documented increase of emergence and re-emergence of zoonotic infectious diseases in Africa in the past years. Thepathogen discovery team at the International Livestock Research Institute (ILRI) addresses the problem in Kenya and beyond. Thegenomics platform at ILRI which is an integration of the bio-repository (Biobank), first and second generation sequencing platformsand high performance computing systems facilitates the pathogen discovery work.PicturesConclusionThe biobank currently has 340,000 samples which include blood, tissues and semen among others from livestock, wildlife, humanand insects collected from East, West and Central Africa among other regions. The genomics platform at ILRI has generated outputsranging from whole/partial genome sequences of Rift Valley fever, Equine Encephalosis, Blue Tongue, African swine fever, Ndumu,Semliki forest, Dugbe, Bunyamwera, Chikungunya, Newcastle disease and Pigeon Paramyxo - viruses among other organismsincluding, bacteria, plants and animals. A number of the genomes are also available to the public on NCBI database.George N. Michukig.michuki@cgiar.org ● Box 30709 Nairobi Kenya ● +254 20 422 3467● www.ilri.orgThis document is licensed for use under a Creative Commons Attribution –Non commercial-Share Alike 3.0Unported License June 2012Presented at the Sequencing, Finishing and Analysis in the Future (SFAF) meeting, Santa Fe, New Mexico, 29-31 May 2013Sampling is a very time-consuming and expensive exercise. We have an ethical and scientific responsibility to make thebest use of that effort and money.Source of samples: Field sampling and collaboratorsCollaborating InstitutionsBio-Bank SystemGenebank, Pubmed(NCBI), MGRASTThe system is under fulltimesurveillance and monitoringMetagenomics platform has first and second generation sequencersThe Bioinformatics platform has 88 computecores, 31TB of network-attached GlusterFSstorage and back up systems.Access to samplesthey have providedProvide samplesto genomicsplatform andreceive back dataData capturedby LIMSProcessed andanalyzed datalinked to sampleLIMS capturesall samplemetadata, storageand all data isbacked upDatatransferredto HPCMetadataand samplesourceSamplelocationAnalyseddata

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