Modules
Slides available on request.
Coordinator: Wiedmann, Martin (NY CoE) mw16 [at] cornell.edu (mw16[at]cornell[dot]edu)
If you have any questions or concerns regarding the modules or webinars, please contact Renato Orsi (rho2 [at] cornell.edu (rho2[at]cornell[dot]edu)).
Access module 1 here.
Learning outcomes
- How different organisms (viruses, bacteria etc.) differ in their genetic material and how this effects interpretation of “genetic subtyping” data
- Different mechanisms of how genetic material changes (substitutions, horizontal gene transfer and recombination, indels) and how this effects interpretation of “genetic subtyping” data
Presenters:
Emilio DeBess (Oregon) and CDC
Access module 3 here.
Learning outcomes
- How NGS differs from traditional Sanger sequencing
- Different sequencing methodologies
- Different quantitative measures used to assess the quality of sequencing data
Presenters:
Madhu Anand and Martin Wiedmann (NY) and CDC
Access module 4 here.
Learning outcomes
- How DNA sequence data can be used to build trees
- Different types of methods to build tress (kSNP)
Presenters:
Madhu Anand and Martin Wiedmann (NY) and CDC
Pathogen Specific Modules
After completion of the module, attendees will know:
- How evolution leads to HIV genetic sequence divergence.
- Basic concepts of genetic sequence alignment and genetic distance.
- How HIV-TRACE uses pairwise genetic distance calculation to define potential transmission clusters.
Presenters:
Joel Wertheim (California, UCSD) and Cheryl Ocfemia (CDC)
Watch the video of the module "Introduction to HIV Evolution"
After completion of the module, attendees will know:
- Key Differences between conventional genotyping and WGS
- What is being represented on a phylogenetic tree
- How WGS is used to assess whether patients are potentially linked by recent transmission.
- Why WGS alone cannot be used to infer direction of transmission
- How TB control programs can use WGS analysis in an investigation
Presenters:
Sarah Talarico and Benjamin Silk (CDC), Tambi Shaw and Martin Cilnis (California DPH)
Watch the videos for "Whole-genome sequencing for investigation of recent TB transmission in the United States":
After completion of the module, attendees will know:
- How WGS is used to detect Listeriosis clusters
- Ways WGS has affected outbreak investigations
- Future directions of WGS relating to Listeria monocytogenes
Presenters:
Matthew Wise (CDC) and Amanda Conrad (CDC)