Evolution of disease genes, fall 2010
Lectures, home assignments and exam.
An alternative option is a seminar (3 cu): no assignments and exam, instead a presentation on a selected topic in week 48 or 49 and a written essay.
The seminar option has been established because of shortage of seminars in MBI-program (Master degree program in bioinformatics) at the moment. Those interested in the seminar option: please give preliminary information about your interest (sirkka-liisa.varvio at helsinki.fi).
It is possible to take both options (7 cu) or only the exam (2 cu) or the assignments (2 cu).
Grading 1-5: Assignments 20 points, exam 40 points. 30/60 points = 1, 50/60 points = 5.
- Wed 3. Nov 12.30-14 C129
- Wed 10. Nov 12.30-14 C129
- Wed 17. Nov 12.30-15 C128
- Wed 1. Dec 12-16 C129, Thu 2. Dec 14-18 B120
- Wed 8. Dec 12.30-16 C129
- Wed 15. Dec 12.30-16 C129
Description of the content
The course aims to provide evolutionary thinking as a complementary framework to medical genetics. Disease gene mapping is one of the mainstreams in bioinformatics. Polymorphisms (for example SNPs, CNVs) are analysed statistically and computationally in order to dissect the components underlying phenotypic traits (for example diseases) from the bulk of all polymorphisms. Most of these are generally thought to be neutral, invisible to natural selection which, simplistically, should promote good and prevent bad genetic variants for invasions and maintenance in populations. Understanding genetic architectures of populations is based on population genetics theory: how stochastic effects (the evolutionary factors ´genetic drift´, small population size, inbreeding, population structures) and natural selection (the darwinian evolutionary factor) shape genomic contents both at the level of populations and at specific sites of molecules. Statistical and computational approaches, based on predictions derived from population genetics theory, aim at dissecting neutral (stochastic) and selected (darwinian natural selection) components of genetic diversity. The selected component includes the genes underlying both adaptive and deleterious traits (unfavourable conditions, diseases). These approaches will be in the course program both at the level of populations (analysis of polymorphisms), as well as at the species level (human specific trait evolution).
Lectures and assignments
- The basic selection model - ASSIGNMENT 1..pdf, 0.5cr
- Thousand genomes news - ASSIGNMENT 2..pdf, 0.5cr
- Deleterious AH-substitutions - ASSIGNMENT 3..pdf, 0.5-1.5cr
Note these: Predicting the effects of AAS.pdf, Non-synonymous SNP phenotyping.pdf
- Inheritance of traits - Pedigree analysis - ASSIGNMENT 4..pdf, 0.5-1cr (half of the exercises or all of them)
- Inheritance of linked genes - recombination - ASSIGNMENT 5..pdf, 0.5cr
- ^Random genetic drift - Inbreeding - .... ASSIGNMENT 6.pdf||\, 0.5cr
Wednesday 8. December (12.30-16) seminar program (somebody missing from the list ?, please inform):
Katherine: Evolutionary costs of positive selection in the human brain
Efthymia: HLA structure and evolution of DR region
Kirsi: Tumour suppressor p53
Benjamin: Tumour suppressor p53
Kim: Vaccine Challenges in the Modern World
Wednesday 15. December (12.30-16) seminar program:
Juha: Celiac disease: What, when, why and how?
Dawit: Celiac …
Mari: Evolution of Brca
Vignesh: Epigenetics of colorectal cancer
Hilal, Mohammad, Fitsum … (somebody missing ?)
Some tentative themes. Topics suggested by students are welcome. This list does not include topics of which negotiations are already ongoing. Topics need not be strictly based on diseases, they can be in the general framework of ´phenotypic trait - genes (or other genomic components) - evolution´, evolution meaning both long term (species level) and population genetic dynamics. Topics below range from long-term evolution (beyond species level) to evolution/population genetics withing the human-lineage (how to explain/model short term evolutionary occurrences). Some of the papers are reviews covering many traits/genes etc. You may pick up some interesting aspect, and focus on that. In addition to the biological substance, include the statistical/computational aspects. Essay should be based ~5 literature references, the length of the essay is ~8 pages. Presentations (45min) during weeks 47 and 48, but deadline for submitting the written essay negotiable.
- Cancer topics:
Tumour suppressor p53.pdf
Evolution of BRCA1.pdf
Evolutionary origins of apoptosis.pdf
- Misc topics:
CYP3A and evolutionary environmental medicine.pdf
Ancestral susceptibility model for common diseases.pdf
Origins and evolution of genetic risk in modern humans.pdf
Evolutionary perspectives in health and medicine.pdf. This paper is an introduction to a set of colloquium papers on evolution/medicine, published in PNAS (Proceeeding of the National Academy of Sciences) January 26, 2010 (suppl 1). Worth looking for finding a topic.
How selection has shaped immunology genes.pdf
Adaptive evolution of genes underlying schizophrenia.pdf
Dog evolution modelling for phenotypic traits.pdf
- Evolution/epigenetics topics.
Is Lamarckian evolution relevant to medicine.pdf
Epigenetics and complex traits.pdf
Epigenetics plasticity disease.pdf
Epigenetics and disease risk.pdf
Timescales of genetics and epigenetics.pdf
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