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Bio-banking and metagenomics platforms for pathogen discovery


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Presented by George N. Michuki 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 forPathogen DiscoveryGeorge N. MichukiInternational Livestock Research Institute (ILRI)Sequencing, Finishing, Analysis in the Future MeetingSanta Fe, New Mexico29-31 May 2013
  2. 2. Introduction• Why pathogen discovery?• Increase of emergence and re-emergence of zoonoticinfectious diseases in Africa• Why Bio-repository (Biobank)?• Sample value and sampling cost - expensive• Why metagenomics?• Looking for what you don’t know• High performance computing systems• High throughput data
  3. 3. The IntegrationDirect fieldcollectionCollaborators(Local/International)BiobankMetagenomics platformHPCLIMSSamplesourcesBackupPC &Amazon NCBI
  4. 4. Sample collection• Use same sample to ask multiple question• Software:• ODK suite - captures metadata• Tarakibu - used to collect GPS laced data as well astime stamped to the second.• Ukasimu - An aliquoting(splitting) system thathelps the field personnel aliquot the samplescollected from the field
  5. 5. The Bio-bank• Currently has 340,000 samples• Samples include: blood, tissues and semen among othersfrom livestock, wildlife, human and insects collected fromEast, West and Central Africa among other regions
  6. 6. AZIZI Monitoring and LIMS system server
  7. 7. AZIZI Monitoring and LIMS system…
  8. 8. • Lab facilities– Safety Levels 1, 2 and 3• Sequencing facilities– 454 sequencer – 2ndGeneration– Three Sanger Capillarysequencers – 1st Generation– MiSeqGenomics platform facilities
  9. 9. • High throughput sampleprocessing– MagnaPure LC Instrument– Magna-lyser• Real time PCR– ABI Real time cyclers7500/7900– Light-cycler nano• HRM analysisGenomics platform facilities
  10. 10. Nucleic Acid ExtractionDNA RNANebulisationRandomLabellingcDNASynthesisFragmented DNA(100bp to 600 bp)Fragmented cDNA(100bp to 600 bp)Nucleic Acid ProcessingBlood/Serum Tissue/vectors Cell Culture SupernatantsMETAGENOMIC APPROACHTargetedapproachTargetedapproach454 Genome Sequencing
  11. 11. • The Bioinformatics platformhas 88 compute cores,• 31TB of network-attachedGlusterFS storage and• back up systems.• Variety of commercial andcustom analysis pipelines - HPC
  12. 12. Analyzed data…/LIMS
  13. 13. BackupYou may call it too much...we call it paranoia... Hourly snapshots of the whole system(external) Daily snapshots of the dbase at 3.15am(internal) Incremental Backups every day (Backuppc) Full Backups every 5 days (Backuppc) Daily dbase snapshots syncd to the cloud Manual backups when updating the dbase Backuppc data saved on a RAID whichprovides increased storage functions andreliability through redundancy“Weve got a good system in place. Guys know their roles, and weve got capable backup. IfMike isnt 100 percent, then Matt will step right in.”
  14. 14. • AVID local database and Genebank:o Dugbe virus,o Semliki Forest virus,o Bunyamwera virus,o Partial Rift Valley Fever viruso Babanki viruso West Nile Viruso Ndumu viruseso Typing of mosquitoes using intron regionsOutputs – project specificG. Michuki. ILRI 14
  15. 15. • None AVID:o ECF vaccine quality check - ILRIo Equine Encephalosis Virus – (OVI – South Africa)o Blue Tongue Virus (OVI – South Africa)o RVF viruses (OVI – South Africa)o New Castle Disease Virus – ILRI – in Genebanko Pigeon Paramyxovirus Virus –KWS – in Genebanko Plasmodium falciparum – Kilifi welcome trusto MHC class 1 and 2 – ILRI vaccine groupo Chikungunya Viruseso Ndumu virus from pigs: - in genebankOutputs with collaboratorsG. Michuki. ILRI 15
  16. 16. Outputs in public….• In Genebank:– Accessions: KC243146.1, JQ217420.1, JQ217419.1, JQ217418.1,JX518532.1, JN989958.1, JN989957.1, ………
  17. 17. • Team:• Steve Kemp – Genomics and ILRI AVID team leader• George Michuki – Wet Lab and bioinformatics• Absolomon Kihara – Database, security and software• Cecilia N. Rumberia – Wet Lab• Alan Orth – Linux support and admin• Anne Fischer – Bioinformatics support (ICIPE-ILRI)Acknowledgements• Funding:•• CGIAR – Research Program on Agriculture for Nutritionand Health
  18. 18. The presentation has a Creative Commons licence. You are free to re-use or distribute this work, provided credit is given to ILRI.better lives through