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 serverhttp://azizi.ilri.cgiar.org/
  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 pipelineshttp://hpc.ilri.cgiar.org/wiki/listofsoftwareBioinformatics - 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:• Google.org• 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 livestockilri.org

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