| Detailed information |
| Original study plan |
Master's programme Biophysics 2023W |
| Objectives |
The aim of this course is to introduce students to different concepts in genetics and evolution applicable to understanding trends in genomic data. Specifically, the course will concentrate on central concepts in population genetics describing the main evolutionary processes changing our genome. The main topics that will be covered are the basic laws of allelic distribution, the processes that change allele frequencies, with special emphasis on mutation and recombination, and the mechanisms of extinction and speciation. The course will be supported by exercises, which are an essential tool to understand the discussed concepts.
Goals
- To provide an introduction to genetics and evolution
- Explain relevant processes in genetics and evolution
- Apply concepts to solve basic exercises
- Learn to information related to evolutionary genetics to understand data structure
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| Subject |
1. Introduction to evolutionary genetics
- Evolutionary history to understand biology today
- The genetic code
- Biological dogma: From genes to proteins
- The structure and organization of DNA
2. Inheritance of genetic information
- Genotype vs phenotype
- The inheritance of DNA
- Meiosis vs. mitosis
- Male vs. female gametogenesis
- Mitochondrial DNA
3. Genome variation
- SNPs and repeats
- Types of SNPs (SNVs)
- Repeats
- Micro- and minisatellites
- Transposons
- Copy number variants (CNVs)
- Segmental duplications
4. Sources of genome variation
- Sources of mutations
- Environmental factors as sources of mutations
- STR process of mutagenesis
- Microsatellites
- Evolution of copy number variants
- Databases of sequence variation (Hapmap)
5. Molecular methods to measure genome variation
- Methods to detect genomic variation
- PCR
- Genotyping (low and large throughput)
- Sequencing
- Next-generation sequencing
- Target enrichment
- Errors in next generation sequencing
- Discovering and assaying variation at tandem repeats
6. Processes that change our genome
- Meiotic recombination ?molecular process
- How does recombination introduce new variations?
- Haplotyping strategies
- Recombination hotspots
- How is recombination inferred?
- Types of recombination
7. Quantifying Genomic variation
- Allele frequency
- Hardy-Weinberg equilibrium
- Chi-square test
- Frequency of heterozygotes
8. Processes that change our genome
- Mutations and allele frequency
- Reversible mutations
- Estimation of mutation rates
- Factors modifying germline mutation rates
9. Processes that change our genome (continued?)
- Neutral evolutionary processes
- Random Genetic drift
- Bottlenecks
- Recombination
- Linkage disequilibrium (D)
- How is LD estimated?
- What is the relationship between LD and recombination?
10/11 Processes that change our genome (continued?)
- Genetic drift-effective population size
- Selection on variation
- Types of selection
- Examples of balancing selection
- MHC
- Malaria and sickle cell anemia
- How does selection change allele frequencies?
- Has selection been acting?
Exercise
- Methods to measure selection in genome data
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| Criteria for evaluation |
Grading
- Exercises: Homework (20%)
- 2 Exams: short answer / multiple choice questions / exercises (80%). Last exam will be cumulative
Exercises: After some lectures a series of exercises will be due for homework (20% of the grade). In addition, every session I will pick somebody to present on the blackboard how a particular exercise was solved.
Exam: There will be two written exams. The last exam will be cumulative. Each exam will count 40% of your grade, 80% in total
Grade scale:
1 90-100;
2 89-80;
3 70-79;
4 60-69;
5 0-59
Attendance: No attendance required for the lectures.
Student resources: I will be recording the sessions so you can listen to the lectures and presentations again.
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| Methods |
Lectures will be combined with exercises explained in class. Exercises will be solved outside of class, but some example questions will be explained on the blackboard. An important aim of the course is also for students to understand how experiments are performed to discover the evolutionary processes in our genome; thus, the course will also discuss methods and techniques to gather data which is analyzed by bioinformaticians.
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| Language |
English |
| Study material |
- Principles of Population Genetics by Daniel Hartl and Andrew Clark ed. (Sinauer, 2nd edition 2009).
- Evolution (CSHL by Nicholas Barton, Derek Briggs, Jonathan Eisen, David Goldstein, Nipam Patel, ed. )
- Human Evolutionary Genetics by Jobling, Mark; Tyler-Smith, Chris; Hollox, Edward; Hurles, Matthew; Kivisild, Toomas. Second Edition (Taylor and Francis CRC.
Also see:
http://www.intechopen.com/books/studies-in-population-genetics
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| Changing subject? |
No |
| Earlier variants |
They also cover the requirements of the curriculum (from - to)
675GTSBTGEK15: KV Topics in Genetics & Evolution (2015W-2019S)
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