General info
This is the homepage for the PhD course "Human population genetic analysis 2011". The course is held by the Department of Biology, University of Copenhagen and is awarded with 5 ECTS point. To sign up, please contact: Rikke (cphsummercourse@gmail.com). The fee for the course is 1800 dkr (approx. US $550) for participants who are not enrolled in a recognized PhD or Master’s program. It is free for PhD and Master's students. The fee does not include food and accommodation.
Content
This course provides a one week comprehensive introduction to a number of topics and common research tools used in analyses of human population genetic data. Topics include: genetic drift, coalescence theory, natural selection, population structure, human disease and evolution, linkage disequilibrium, association mapping, genomic control, haplotype structure, IBD mapping, admixture mapping, genotyping data, re-sequencing data, phasing and imputation, HapMap data, 1000 genomes project, online resources.
Instructors
- Rasmus Nielsen (UC Berkeley/University of Copenhagen)
- Andrew G. Clark (Cornell University)
- Mark Beaumont (University of Reading)
- Line Skotte (University of Copenhagen)
- Ida Moltke (University of Copenhagen)
- Anders Albrechtsen (University of Copenhagen)
Time and place
The course is taught from June 20 to June 24 2011. All five days there will be lectures at the H.C. Oersted Institute, Universitetsparken 5 in auditorium 6.
Course material
Handouts will be passed out during the course, but for each lecture there is one or two articles/notes that should be read in advance. There are password protected links for handouts in the right bar (will be available before the lecture) and links for the articles/notes in the program below. If you are not used to working with probability we also recommend that you read these notes.
Program suggestion
Monday
- 09:00 - 09:10 Registration.
- 09:10 - 10:15 Lecture 1: Population genetics; drift and coalescence theory part I (Rasmus Nielsen) reading reading
- 10:30 - 12:00 Exercise I (DnaSP)
- 12:00 - 01:00 Lunch (on your own)
- 01:00 - 02:15 Lecture 2: Population genetics; drift and coalescence theory part II (Rasmus Nielsen) reading
- 02:30 - 04:00 Computer Exercise II (DnaSP)
- 04:15 - 05:00 Research Lecture by Jotun hein (Oxford University) : Combinatorial Approaches to Ancestral Recombination Graph Reconstruction.
- 05:00 - 07:30 Reception
Tuesday
- 09:00 - 10:15 Lecture 3: Population genetics; demography (Mark Beaumont) reading reading reading
- 10:30 - 12:00 Computer Exercises III (DnaSP)
- 12:00 - 01:00 Lunch (on your own)
- 01:00 - 02:15 Lecture 4:Population genetics; natural selection (Rasmus Nielsen) reading reading reading
- 02:30 - 04:00 Computer Exercises IV
- 04:15 - 05:00 Research Lecture by Mark Beaumont (University of Reading): TBA.
Wednesday
- 09:00 - 10:15 Lecture 5: Recombination and linkage disequilibrium (Mark Beaumont) reading
- 10:30 - 12:00 Computer Exercise V
- 12:00 - 01:00 Lunch (on your own)
- 01:00 - 02:15 Lecture 6: Association studies (Anders Albrechtsen/Line Skotte) reading
- 02:30 - 04:00 Computer Exercises VI
- 04:15 - 05:00 Research Lecture by Tom Gilbert (Copenhagen University): The molecular hunt for the giant squid.
Thursday
- 09:00 - 10:15 Lecture 7: Genome-wide association studies (Andrew G. Clark) reading
- 10:30 - 12:00 Computer Exercises VII
- 12:00 - 01:00 Lunch (on your own)
- 01:00 - 02:15 Lecture 8: Next generation sequencing (Anders Albrechtsen,Line Skotte) reading
- 02:30 - 04:00 Computer Exercises VIII
- 04:15 - 05:00 Research Lecture by Niels Grarup (University of Copenhagen): Large-scale sequencing of our genomes to identify risk elements in human metabolic disease.
Friday
- 09:00 - 10:15 Lecture 9: Phasing and imputation (Andrew G. Clark) reading
- 10:30 - 12:00 Computer Exercise IX
- 12:00 - 01:00 Lunch (on your own)
- 01:00 - 02:15 Lecture 10: Relatedness and Admixture mapping (Ida Moltke) reading
- 02:30 - 04:00 Exercises X
- 04:15 - 05:00 Research Lecture by Andrew G. Clark (Cornell) : Population genetic consequences of explosive population growth.
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.