Cloud Computing and NGS data analysis course - problem definition

Slides of the “problem definition: outbreak pathogen identification” session by [Marina Manrique](http://ohnosequences.com/mmanrique), from the Cloud Computing and NGS Data Analysis course we organized in August 2013, as part of the INTERCROSSING International Training Network.

http://ohnosequences.com/slides/intercrossing-course

Transcript

1. Raquel Tobes Marina Manrique Eduardo Pareja-Tobes 2013-08-26 Problem definition
2. content • intro • problem • background & general concepts • guidelines • week plan • teams
3. Problem Design a system to rapidly characterize and identify the pathogen responsible for an outbreak
4. Based on NGS and Cloud Computing
5. Background & general concepts • what is an outbreak? • impact • outbreaks and NGS
6. What is an outbreak? “Outbreak is a term used in epidemiology to describe an occurrence of disease greater than would otherwise be expected at a particular time and place.” Wikipedia
7. What is an outbreak? Normally caused by an infectious agent Virus Bacteria Fungi
8. What is an outbreak? Healthcare associated Community acquired
9. What is an outbreak?
10. What is an outbreak?
11. What is an outbreak?
12. What is an outbreak? Antibiotic resistant bugs High-risk clones
13. What is an outbreak?
14. What is an outbreak? Extension: Really local (ICU) Worldwide
15. What is an outbreak? Local
16. What is an outbreak? Worldwide
17. What is an outbreak? Worldwide
18. Impact A real impact on public health
19. Impact Avian flu H1N1 CDC estimates • 61 million people infected with 2009 H1N1 • 274,000 2009 H1N1-related hospitalizations • 12,470 2009 H1N1-related deaths http://www.cdc.gov/h1n1flu/estimates_2009_h1n1.htm
20. Impact Multistate Fungal Meningitis Outbreak Current outbreak in the States Healthcare associated infection. Non contagious http://www.cdc.gov/hai/outbreaks/meningitis.html
21. Impact Multistate Fungal Meningitis Outbreak
24. Impact Multistate Fungal Meningitis Outbreak
26. Impact Multistate Fungal Meningitis Outbreak This is just a real case of how an outbreak is tracked
27. Impact Multistate Fungal Meningitis Outbreak This is just a real case of how an outbreak is tracked Where the detection is based on PCR and sequencing But what if...
28. Impact Multistate Fungal Meningitis Outbreak -The agent is not well characterized? We don’t have this set of primers or they don’t work nicely - The agent is spreading (even) much faster than expected? We need quicker ways to identify it
29. Impact NGS and Cloud Computing could help here?
30. Outbreaks and NGS Quickly characterize the pathogen and identify it
31. Outbreaks and NGS Quickly characterize the pathogen and identify it That’s a fact today
32. Outbreaks and NGS
33. Outbreaks and NGS
34. Outbreaks and NGS
35. Outbreaks and NGS EHEC German outbreak 2011 A real example of how NGS was used for characterizing the pathogen and designing primers to detect it
36. Outbreaks and NGS
38. * * *
39. * * * genomic data available Detection kit protocol
40. * * Detection kit protocol
41. * * Detection kit protocol NGS
43. http://bgiamericas.com/bgi-releases-a-complete-de-novo-e-coli-o104-genome-ass embly-and-is-making-their-detection-kit-protocols-and-synthesized-primers-fre ely-available-to-worldwide-disease-control-and-research-agencies/
44. Outbreaks and NGS EHEC German outbreak 2011 Detection kit protocols and synthesized primers available In 16 days from the announcement of the outbreak In only 6 days from the release of the first genomic data
45. Outbreaks and NGS So yes, NGS may be (and is) useful in this field in at least to steps: 1. Genome Characterization 2. Pathogen detection
46. Outbreaks and NGS What about Cloud Computing?
47. Guidelines NGS: your design should have an answer for Rapid characterization of the pathogen causing the outbreak - How would you characterize the pathogen? De novo assembly of the genome + annotation? MLST? Searching for virulence proteins exclusively? All, none? - How quick you can do it once you have the sequences? - Your design is scalable?
48. Guidelines NGS: your design should have an answer for Rapid identification of the pathogen in samples - You have the agent characterized, how you’d identify it? - The identification would be based on PCR? Whole genome sequencing?
49. Guidelines Some general questions you should address in the design - Which sequencing technology (or combination of them) would you use? - Which samples requirements you would have? Could you work with clinical samples? really low DNA quantity with poor quality? Would you need a prior phase of pathogen isolation and growth? - How long the whole process would take (wet lab + data analysis)?
50. Guidelines The more realistic and detailed the better. It’s a design and research task. There’s not a unique correct solution for it
51. Week plan
52. Teams Team 1 Kim Om Andrea Habib Team 2 Fabian Lizzy Alexandre Alexandra Vedran Team 3 Alexey Jeannine Jasmin Somya
53. Data sets https://github.com/ehec-outbreak-crowdsource d/BGI-data-analysis/wiki/Sequence-reads