General info
This is the homepage for the PhD course "PhD course in analyses of genotyping and next-generation sequencing data in medical and population genetics 2016". The course is held by the Department of Biology, University of Copenhagen and is awarded with 5 ECTS point. To sign up, please contact us at cphsummercourse@gmail.com. The course is free for all PhD students at Danish universities (KU, AU, AUC, SDU and DTU). For all other PhD students there is a course fee of 200 US dollars. Food and accommodation are not included in the course.
Content
The course is a comprehensive introduction to a number of topics and common research tools used in analyses of genetic data. Topics include: genetic drift, natural selection, population structure, Fst, linkage disequilibrium, relatedness, association mapping, GWAS, genotyping data, next-generation sequencing (NGS) data, 1000 genomes project data. The main focus will be on humans, but the methods are applicable for 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
- Laura Rodriguez Botigue (Stony Brook University)
- Matteo Fumagalli (University College London)
- Fernando Racimo (New York Genome Center)
- Kasper Munch (Aarhus University)
- Thorfinn Sand Korneliussen (University of Copenhagen)
- Line Skotte (Statens Serum Institut)
- Anders Albrechtsen (University of Copenhagen)
- Ida Moltke (University of Copenhagen)
Time and place
The course will take place from August 22nd to August 26th 2016 at Biocenteret, Ole Maaloes Vej 5, 2200 Copenhagen N. All lectures and computer exercises will take place in room 4.0.02 (building 4, ground floor, room number 02).
Laptop
You should bring a laptop to the course. We will log into a remove server from the laptop so any laptop will do regardless of operating system. However, please, if at all possible, make sure your computer can be connected to wired internet.
Course material
Handouts will be passed out during the course, but for some of the lectures there are articles/notes that should be read in advance - you can find them here. The slides used during the lectures will be made available right before the lectures.
Program
Monday - Introduction to population genetics
- 09:00 - 09:10 Registration.
- 09:15 - 10:15 Lecture 1: Introduction to basic population genetic terms and concepts (Fernando)
- 10:30 - 12:00 Computer exercise I: (Fernando)
- 12:00 - 01:00 Lunch (on your own)
- 01:00 - 02:15 Lecture 2: Introduction to basic population genetic terms and concepts II (Kasper)
- 02:30 - 04:00 Computer Exercise II:
- 04:15 - 05:00 Research lecture by Kasper Munch
- 05:00 - 07:30 Reception/social mixer
Tuesday - Introduction to NGS data
- 09:00 - 10:15 Lecture 3: Data processing, mapping, and filtering. (Thorfinn)
- 10:30 - 12:00 Computer Exercises III: (Thorfinn)
- 12:00 - 01:00 Lunch (on your own)
- 01:00 - 02:15 Lecture 4: Estimation of allele frequencies, SNP calling and genotype calling, from NGS data (Matteo+Anders)
- 02:30 - 04:00 Computer Exercises IV: (Matteo + Anders)
- 04:15 - 05:00 Research lecture by Matteo Fumagalli
Wednesday - Inference of demographic history and population structure
- 09:00 - 10:15 Lecture 5: Demographic inference (Fernando)
- 10:30 - 12:00 Computer Exercise V: e.g. IM, DADI , ANGSD, and ngsTools (Fernando)
- 12:00 - 01:00 Lunch (on your own)
- 01:00 - 02:15 Lecture 6: Inference of population structure (Laura)
- 02:30 - 04:00 Computer Exercises VI: (Laura)
- 04:15 - 05:00 Research lecture by Fernando Racimo
Thursday – Disease mapping
- 09:00 - 10:15 Lecture 7: Association mapping I. Introduction to association mapping (Ida)
- 10:30 - 12:00 Computer Exercises VII: (Ida)
- 12:00 - 01:00 Lunch (on your own)
- 01:00 - 02:15 Lecture 8: Association mapping II. Whole genome NGS association and dealing with population structure (Anders+Line)
- 02:30 - 04:00 Computer Exercises VIII: (Anders)
- 04:15 - 05:00 Research lecture by Ida Moltke
Friday - Detecting selection and genetic load
- 09:00 - 10:15 Lecture 9: Detecting natural selection (Matteo)
- 10:30 - 12:00 Computer Exercise IX (Matteo)
- 12:00 - 01:00 Lunch (on your own)
- 01:00 - 02:15 Lecture 10: Distribution of genetic load (Laura)
- 02:30 - Short Exercises (Laura)
- 03:15 - 04:00 Research lecture by Laura Rodriguez Botigue
- 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.