|
Module title
|
After completion of the module, attendees will know…
|
Presenter(s) |
(1) Genetics & evolution 101
(15.6 MB file) |
- 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
|
Emilio DeBess (Oregon)
and CDC |
(2) Intro to next gen sequencing methodologies (NGS)
(41.5 MB file) |
- How NGS differs from traditional Sanger sequencing
- Different sequencing methodologies
- Different quantitative measures used to assess the quality of sequencing data
|
Matthew Schimenti (Florida); Paul Cieslak (Oregon) and CDC |
(3) Introduction to sequence analyses
(17.8 MB file) |
- How NGS data are assembled into contigs
- The difference between de novo and reference-based assemblies
- How two sequences are compared to determine the level of similarity
|
Madhu Anand and Martin Wiedmann (NY) and CDC |
(4) Tree building 101- how to visualize genetic relatedness between large sets of individuals
(63.6 MB file) |
- How DNA sequence data can be used to build trees
- Different types of methods to build tress (kSNP)
|
Madhu Anand and Martin Wiedmann (NY) and CDC |
Pathogen Specific Modules
|
| Module title |
After completion of the module, attendees will know… |
Presenter(s) |
| (1) Introduction to HIV Evolution |
- 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.
|
Joel Wertheim (California, UCSD)
and Cheryl Ocfemia
(CDC) |
|
Whole-genome sequencing for investigation of recent TB transmission in the United States: Current uses and future plans
Part 1 | Part 2 | Part 3
|
- 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
|
Sarah Talarico
and Benjamin Silk (CDC), Tambi Shaw and Martin Cilnis (California DPH) |
| Use of Routine Whole Genome Sequencing to Improve Investigation of Listeriosis Outbreaks |
- How WGS is used to detect Listeriosis clusters
- Ways WGS has affected outbreak investigations
- Future directions of WGS relating to Listeria monocytogenes
|
Matthew Wise (CDC) and Amanda Conrad (CDC) |