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TALES FROM THE DEEP

the infectious disease landscape. TALES FROM THE DEEP. how deep sequencing is changing . dr. jennifer gardy leader, molecular epidemiology bc centre for disease control jennifer.gardy@bccdc.ca @ jennifergardy. Disclosures. Honoraria from: CACMID, Trent University, CDC Atlanta

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TALES FROM THE DEEP

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  1. the infectious disease landscape TALES FROM THE DEEP how deep sequencing is changing dr. jennifergardy leader, molecular epidemiology bc centre for disease control jennifer.gardy@bccdc.ca @jennifergardy

  2. Disclosures • Honoraria from: CACMID, Trent University, CDC Atlanta • Research support from: Provincial Health Services Authority, Genome British Columbia, Genome Canada, CIHR, First Nations and Inuit Health

  3. figure 1. gregormendel.

  4. inheritance

  5. figure 2. friedrichmiescher. 1869.

  6. DNA’s chemistry phoebuslevine 1919 williamastbury 1937

  7. DNA is the hereditary material

  8. photo 51. 1952 franklin & gosling

  9. watson & crick

  10. fredericksanger. 1977.

  11. dideoxy sequencing, or chain-termination, looks at end-labelled fragments of DNA to deduce the sequence.

  12. machines like this… …generate output like this

  13. first genome sequenced. h. influenzae, 1995.

  14. hundreds of machines

  15. thirteen months

  16. $900,000

  17. figure 3. genome projects in GOLD.

  18. a change in technology

  19. sequencing by synthesis enables massively parallel sequencing in real time.

  20. THE PLAYERS life tech. aka ion torrent PGM ionproton illumina aka solexa miseq hiseq GA roche aka 454 GS flex GS junior oxford nanopore minion gridion

  21. figure 4a. a handy comparison.

  22. figure 4b. a handier comparison. 384,000 bases/day 300 years/human genome VERSUS 600,000,000,000 bases/day 1 day/human genome

  23. we can sequence hundreds of bacterial genomes

  24. or all the viral quasispecies inone host

  25. 1. reconstruct outbreaks of communicable disease PMID: 21345102

  26. 2. understand epidemic dynamics PMID: 20142485

  27. 3. describe a novel pathogen PMID: 21793740

  28. 4. develop new molecular typing methods PMID: 22135463

  29. 5. understand antimicrobial resistance unpublished data

  30. 6. date the time of infection PMID: 218322936

  31. 7. date the emergence of a pathogen PMID: 20025195

  32. 8. therapeutic monitoring of drug resistance PMID: 20628644

  33. 9. describe co-infections PMID: 21326348

  34. 10. discover new pathogens or biomarkers PMID: 20463061

  35. so, what’s the catch?

  36. buried alive by data

  37. THANK YOU

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