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.
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.
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.
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.
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/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 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 | Lecture | Exercise |
|---|---|---|
| 5 | Course intro and overview, Coop chapt 1, 2, 3, Paper: Simons Genome Diversity Project | Cluster practicals |
| 6 | Drift and the coalescent, Ancestral recombination graph (ARG), Coop chapt 4; Paper on Platypus | Read mapping and base calling |
| 7 | Past population demography, HMMs, ARG, Paper on PSMC | Estimating past population sizes |
| 8 | Recombination, Phasing, HMMs, ARG, PSMC Paper on tree inference, Review on recombination rate | Phasing and recombination |
| 9 | Population structure, Incomplete lineage sorting, HMMs, Coop chapt 6, Review on ILS | Inference of population structure and admixture |
| 10 | Admixture, HMMs, Review on admixture, Paper on admixture inference | |
| 11 | Tree sequences | Tree sequences |
| 12 | Direct and linked selection, Coop chapt 12, 13, revisit Paper on tree inference | Inference of positive selection |
| 13 | Projects, Popgen overview, Mandatory project description | GWAS quality control |
| 14 | GWAS review, Population stratification review, Coop 99-120 (No Exercise this week) | Association testing |
| 15 | Heritability, Review on heritability and LMM ; Coop Sec 2.2 (p23-36) + Chapt 7 (p119-142) | Estimating heritability |
| 16 | Break | Break |
| 17 | Break | Special lecture: GWAS meets ARGs, Evolution and disease Coop Sec. 11.0.1 (p217-221), Paper on exploiting ARGs in GWAS |
| 18 | Genomic pre-trained networks | Project guidance |
| 20 | Chromatin structure and epigenetics | Project guidance |