Population genomics course

Description

After the course, the participants will have detailed knowledge of the methods and applications required to perform a typical population genomic study.

The participants must, at the end of the course, be able to:

• Identify an experimental platform relevant to a population genomic analysis.
• Apply commonly used population genomic methods.
• Explain the theory behind standard population genomic methods.
• Reflect on the strengths and limitations of population genomic methods.
• Interpret and analyze results of population genomic inference.
• Formulate population genetics hypotheses based on data

The course introduces fundamental concepts in population genomics, from generating population genetic data sets to the most common population genetic analyses and association studies. The course's first part focuses on generating population genetic data sets. The second part introduces the most common population genetic analyses and their theoretical background. Here, topics include analysis of demography, population structure, recombination, and selection. The last part of the course focuses on applications of population genetic data sets for association studies relating to human health.

Curriculum

The curriculum for each week is listed below. "Coop" refers to a set of lecture notes by Graham Coop that we will use throughout the course.

Padlet

We will use a padlet for shared communication about the curriculum. There, I may post questions to guide your studies, and you can comment on which parts of the curriculum you find most challenging so we can focus on that.

link to padlet

Access to the computing cluster

You will do the exercises on the GenomeDK computing cluster. So before the course begins, you must request a user account by applying here. You need to fill in some information. Most of it is self-explanatory. For "Organization" fill in "Aarhus University", for "Department" fill in "BiRC", for "Zone" choose "Open", for "Reason" fill in "Population genomics course", for "Username" fill in a short username that you think might be unique.

Student presentations

You will each do two student presentations together with a fellow student. You should sign up for one presentation in the first half of the course and one in the last half. In this Google Sheet, you can see the available dates and the topics to choose from on each date. Fill in your name as "student one" or "student two" for two dates.

Lectures

Lectures/discussions are on Mondays from 12:15 to 15:00. You can see the curriculum for each lecture in the weekly plan below. Each lecture session will be structured like this:

• 10-minute student presentation on a topic related to the past week's curriculum.
• 10-minute student presentation on a topic connected to the past week's week's curriculum.
• 30-minute lecture based on the current week's curriculum.
• 15 break
• 45-minute lecture/discussion on the current week's curriculum.
• 15 break
• 45-minute lecture/discussion on the current week's curriculum.

Exercises

Exercises are on Thursdays from 12:15 to 14:00. The week plan below has links to the exercises hosted on the GitHub page for the course.

Week plan

1. Course intro and overview:
   • Lecture (Kasper): Coop chapters 1, 2, 3, Paper: Simons Genome Diversity Project
   • Exercise (Bjarke): Cluster practicals
2. Drift and the coalescent, Ancestral recombination graph:
   • Lecture (Kasper): Coop chapter 4; Paper about Platypus,
   • Exercise (Bjarke): Read mapping and base calling
3. Past population demography, HMMs, Ancestral recombination graph, :
   • Lecture (Kasper): Paper about PSMC
   • Exercise (Bjarke): Estimating past population sizes
4. Recombination, Phasing, HMMs, Ancestral recombination graph, PSMC:
   • Lecture (Kasper and Juraj): Paper about tree inference, Review about recombination rate estimation
   • Exercise (Bjarke): Phasing and recombination
5. Population structure, Incomplete lineage sorting, HMMs:
   • Lecture: Coop chapter 6, Review about incomplete lineage sorting
   • Exercise: Inference of population structure and admixture
6. Admixture, HMMs:
   • Lecture (Kasper): Review about admixture, Paper about admixture inference
   • Exercise (Bjarke): Detecting archaic ancestry in modern humans
7. Tree Sequences:
   • Lecture (Kasper): Paper about tree inference,
   • Exercise (Bjarke): Tree sequences
8. Direct and linked selection:
   • Lecture: Coop chapters 12, 13, revisit Paper about tree inference
   • Exercise (Bjarke): Inference of positive selection

• Thursday lecture April 4. 13:15-15:00:
  • Lecture (Søren): GWAS review, Population stratification review, Coop lecture notes 99-120.
  • (No Exercise this week)

9. Heritability:
   • Lecture (Søren): Missing heritability and mixed models review ; Coop Lecture notes Sec. 2.2 (p23-36) + Chap. 7 (p119-142)
   • Exercise (Bjarke): GWAS quality control
10. Evolution and disease:
    • Lecture (Søren): Genetic architecture review ; Article about "omnigenic" model ; Coop Lecture notes Sec. 11.0.1 (p217-221)
    • Exercise (Bjarke): Association testing
11. TBA:
    • Lecture: TBA
    • Exercise (Bjarke): Estimating heritability
12. Project presentations:
    • Lecture (Kasper, Søren): None
    • Exercise (Bjarke): None. Focus on projects
13. Project guidance:
    • Lecture (Kasper, Søren): None
    • Exercise (Bjarke): None. Focus on projects
14. Project guidance:
    • Lecture (Kasper, Søren): None
    • Exercise (Bjarke): None. Focus on projects