Kemp, Stephen J.

Kihara, Absolomon

Michuki, G.

Orth, Alan S.

Rumberia, C.

CGSpace

Bio-banking and Metagenomics Platforms for Pathogen Discovery at ILRI George Michuki, Absolomon Kihara, Alan Orth, Cecilia Rumberia and Steve Kemp Introduction There has been documented increase of emergence and re-emergence of zoonotic infectious diseases in Africa in the past years.  The pathogen discovery team at the International Livestock Research Institute (ILRI) addresses the problem in Kenya and beyond. The genomics platform at ILRI which is an integration of the bio-repository (Biobank), first and second generation sequencing platforms and high performance computing systems facilitates the pathogen discovery work. Pictures Conclusion The biobank currently has 340,000 samples which include blood, tissues and semen among others from livestock, wildlife, human and insects collected from East, West and Central Africa among other regions. The genomics platform at ILRI has generated outputs ranging 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 organisms including, bacteria, plants and protozoan parasites. A number of the  genomes are also available to the public on NCBI database. George N. Michuki  g.michuki@cgiar.org ● Box 30709 Nairobi  Kenya  ●  +254 20 422 3467  ● www.ilri.org    This document is licensed for use under a Creative Commons Attribution –Non commercial-Share Alike 3.0 Unported License  June 2012 August 24-29, 2014 for TTP8/STVM12  Sampling is a very time-consuming and expensive exercise. We have an ethical and scientific responsibility to make the best use of that effort and money. Source of samples: Field sampling and collaborators Collaborating Institutions Bio-Bank  System Genebank, Pubmed (NCBI), MGRAST The system is under fulltime surveillance and monitoring Metagenomics platform has first and second generation sequencers The Bioinformatics platform has 88 compute cores, 31TB of network-attached GlusterFS storage and back up systems. Access to samples they have provided Provide samples to genomics platform and receive back data Data captured by LIMS Processed and analyzed data linked to sample LIMS captures all sample metadata, storage and all data is backed up Data transferred to HPC Metadata and sample source Sample location Analysed data 

Bio-banking and metagenomics platforms for pathogen discovery at ILRI

https://cgspace.cgiar.org/bitstream/10568/42182/1/TTP8_Michuki_2014.pdf

Bio-banking and metagenomics platforms for pathogen discovery at ILRI

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