2021
General info
Date: July 26-30 2021
Place: Copenhagen Denmark
Organized by: The Department of Biology and the Globe Institute, University of Copenhagen (Fernando Racimo, Anders Albrechtsen and Ida Moltke)
Price: Free for all PhD students at Danish universities. 200 USD for all other students.
Includes: All teaching. Food and accommodation are NOT included in the course fee.
Contact and sign up: Signup is closed - To signup please fill in the questionaere, for questions write to cphsummercourse@gmail.com
Corona and disclamer
Due to corona we know that some of you might have issues traveling to the course and we might have to make changes to the course. We will keep you updated as we get closer to the starting date.
Content
The course is a comprehensive introduction to a number of topics and common research tools used in analyses of next-generation sequencing (NGS) data. Topics include: genetic drift, natural selection, population structure, association mapping, GWAS, spatial genetics, f-statistics and demographic inference. The main focus will be on humans, but the methods we will cover are applicable to many other species as well. Lectures will be combined with hands-on computer exercises, mostly using R and command-line based programs.
Intended Learning Outcome
After the course the student should be able to:
- Use population genetic theory to infer basic population genetics characteristics from genetic data, including Fst, population size, relatedness and linkage disequilibrium
- Be able to infer ancestry and population structure based on genetic data
- Use NGS data including low depth for population genetic inference.
- Select the optimal strategy for disease mapping based on the available data, the trait of interest, and the population genetics characteristics of the sample population, including taking population structure into account
- Interpret and discuss the results of own analyses and results in the scientific literature
Instructors
- Benjamin Peter, Group leader, Max Planck Institute for Evolutionary, Germany
- Tyler Linderoth, Research Associate, University of Cambridge
- John Novembre, Professor, Department of Human Genetics, Department of Ecology & Evolution, University of Chicago
- Shilpa Garg, Group leader, Department of Biology, University of Copenhagen, Denmark
- Fernando Racimo, Group leader, Globe Institute, University of Copenhagen, Denmark
- Anders Albrechtsen, Group leader, Department of Biology, University of Copenhagen, Denmark
- Ida Moltke, Group leader, Department of Biology, University of Copenhagen, Denmark
Time and place
The course will take place from July 26 to July 30th 2021 at Biocenteret, Ole Maaloes Vej 5, 2200 Copenhagen N. All lectures and computer exercises will take place in room 4.0.24 (i.e. building 4, ground floor, room number 24). This includes research talks.NB. The main entrance to the Biocenter is likely locked in July. Instead you should be able to enter using the back entrance shown on this map. Notice that to get to the back entrance you need reach the building from a different street (Jagtvej).
Laptop
You should bring a laptop to the course. We will log into a remote server from the laptop so any laptop will do regardless of operating system.
Course material
The lecture will be based on a large amount of reading material (articles/notes) that should be read in advance - you can find them here once they are finalized (you will get an email with password). The slides used during the lectures will be made available right before the lectures.
Program (2021)
Monday - Introduction to population genetics and NGS data
- 09:00 - 09:15 Welcome (Ida Moltke)
- 09:15 - 10:15 Lecture 1: Introduction to basic population genetic terms and concepts (Fernando Racimo)
- 10:30 - 12:00 Computer exercises I
- 12:00 - 01:00 Lunch (on your own)
- 01:00 - 02:15 Lecture 2: Introduction to basic NGS data, Data processing, and formats (Tyler Linderoth)
- 02:30 - 03:15 Computer exercises II
- 03:30 - 04:15 Research lecture by Rute Fonseca, UCPH. Title: "Using NGS data across different time scales"
- 04:30 - 07:00 Reception/social mixer
Tuesday - Analysis of NGS data and population structure
- 09:00 - 10:15 Lecture 3: Estimation of allele frequencies, SNP calling and genotype calling from NGS data (Tyler Linderoth)
- 10:30 - 12:00 Computer exercises III
- 12:00 - 01:00 Lunch (on your own)
- 01:00 - 02:15 Lecture 4: Inference of population structure (John Novembre)
- 02:30 - 04:00 Computer exercises IV
- 04:15 - 05:00 Research lecture by Tyler Linderoth, Cambridge Title: "Mapping the genetic routes to extreme diversification and sex determination in East African cichlid fishes using thousands of genomes"
- Canal boat trip
Wednesday - Inference of demographic history
- 09:00 - 10:15 Lecture 5: D/f/F statistics (Ben Peter)
- 10:30 - 12:00 Computer exercises V
- 12:00 - 01:00 Lunch (on your own)
- 01:00 - 02:15 Lecture 6: Spartial population structure (John Novembre)
- 02:30 - 04:00 Computer exercises VI
- 04:15 - 05:00 Research lecture by Shilpa Garg, UCPH, Title "Advanced approaches for chromosome-scale phasing."
Thursday – Demography and selection
- 09:00 - 10:15 Lecture 7: Admixture graphs and spatial methods (Ben Peter)
- 10:30 - 12:00 Computer exercises VII
- 12:00 - 01:00 Lunch (on your own)
- 01:00 - 02:15 Lecture 8: Selection scans (Anders Albrechtsen)
- 02:30 - 04:00 Computer exercises VIII
- 04:15 - 05:00 Research lecture by John Novembre, U. Chicago. Title "New tools and models for geographic structure in population genetic data"
Friday - Disease mapping and selection
- 09:00 - 10:15 Lecture 9: Association mapping I. Association mapping and GWAS (Anders Albrechtsen/Ida Moltke)
- 10:30 - 12:00 Computer exercises IX
- 12:00 - 01:00 Lunch (on your own)
- 01:00 - 02:15 Lecture 10: Selection - temporal/aDNA (Fernando Racimo + Evan Irving-Pease)
- 02:30 - 04:00 Computer exercises X
- 04:15 - 05:00 Research lecture by Benjamin Peter, Max Planck, Leipzig, Title "Methods for modelling complex population structure"
- 05:00 - ? Farewell drinks
Evaluation
Participants who have participated actively in all parts of the course and completed all exercises satisfactorily will be awarded a certificate of completion at the end of the course. The work load corresponds to 5 ECTS points. Note that this workload includes one week of preparation. Reading material for this is available in the above course program.