Molecular Epidemiology and Sequencing Approaches in Public Health - Modules

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