Project-Cooties

Jake A Lacey

Teaching and Training Resources for Genomic Epidemiology and Pathogen Genomics using Fictitious Diseases

This resouce was inspired by the Genomic Epidemilogical Handbook written by Allison Black and Gytis Dudas https://alliblk.github.io/genepi-book/index.html, which provides a fabulous background into the concepts and theory of genomic epemiology. Where this resource diverts is providing to practial hands on genomic-epidemiolgoy analysis.

If you are interested in the history of epidemiology or if this is your very first exposure to genomic epidemiology I would recomend listeing to this epidsode of "This podcast will kill you" by the Erins https://thispodcastwillkillyou.com/2022/05/10/special-episode-on-the-origin-of-epidemiology/ and reading the book above.

Who is this resource for?

Resource for teaching and training the concepts genomic epidemiology including

1. Epidemiological analysis and concepts
2. Genomics/Bioinformatics analysis and concepts
3. Outbreak detection and public health surveillance
4. Large scale data analysis

This resource will be useful for:

• Public health microbiologists developing a genomic surveillance program.
• Bioinformaticians working in public health, and wanting to increase their familiarity with genomic epidemiology.
• Epidemiologists who want to integrate genetic information as well.
• Health officers or other policy makers who want to understand more about pathogen genomic data as a source of epidemiological information.
• Academics collaborating with with a public health institution who want to learn more about genomic epidemiology in applied public health settings (It might be more different than you think).
• Newly established public health systems (remote and under resourced settings) building or expanding their current capacity

This resource will is NOT:

• Not provide an exhaustive description of all the questions that scientists can investigate with genomic epidemiology
• Not teach how to control or implement interventions against infectious disease
• We will not present every method for genomic epidemiological analysis, nor will we provide information on the entire suite of available analytic tools. You don't need a know how a hammer is made and the physics behind it for a hammer to be useful. Especially if you use it for its intended purpose. If you start using a hammer ad a screw driver then that's on you.
• Not discuss pathogen specific metrics or analysis that can be used in public health

This will be achieved by teaching the concepts of genomic epidemiology via an entirely fictional pathogen (cooties virus)

• Use simulated epidemiological data and outbreak datasets including census data and medical data
• Use simulated genetic data (Viral genome, sequence reads, and SNP data)