2010-2011 academic year
Genomics (20440)
Qualification/course: bachelor's degree in Human Biology
Year: third
Term: third
Number of ECTS credits: 4 credits
Student commitment: 100 hours
Teaching language or languages: Catalan and English
Teaching staff: Jaume Bertranpetit, coordinator; Elena Bosch, Francesc Calafell, David Comas, Roderic Guigó, Hafid Laayouni, Tomàs Marquès-Bonet, Arcadi Navarro and Ricard Solé
1. Introduction to the subject
Genomics describes the determination of the nucleotide sequence and all analyses possible used to discover the functional and structural information contained in the genome as a whole (including the genes) of any organism. The objective of the subject is to understand the basic structure of the genome, its functional implications and the dynamic and evolution of genomes, with special emphasis on the human genome. The methods and results of genomic analysis will be presented, and the implications of this type of research discussed. The subject will cover the emergence of new ultrasequencing technologies and biocomputing tools for understanding the dynamic and evolution of any genome. It also includes concepts of microbial ecosystem metagenomics and the latest applications in the study of the human genome. It will therefore include concepts of basic biological sciences, computer sciences, biotechnology, biocomputer science and epidemiology. The initial requirements are some basic knowledge of molecular biology, genetics, statistics, biocomputer science and evolution.
2. Competences to be acquired
3. Contents
1. The situation of genomics in 2010. A general view
Discovering the sequence of genomes.
2. Genomes, transcriptomes and proteomes.
3. Studying DNA. Genetic and physical maps
4. Genome sequencing
DNA sequencing methodology. Ultrasequencing technologies and their future. Assembly of an adjacent sequence.
5. Some of the main genomic projects and the lessons learnt from them. The human genome project. Technology and social implications. Potential for medicine and other contributions.
Genome anatomy: composition, architecture.
6. Prokaryote genomes. The initial sequence of bacteria. The current state of metagenomics
7. Nuclear eukaryote genomes. The structure of chromosomes. Genome composition and organisation
8. The prokaryote genome and eukaryote organelles. Genomics of microbial communities
9. Genomes of viruses and mobile transferrable elements
10. Genome annotation. Techniques and databases
Functional genomics.
11. The structure of the nucleus and chromatin. Large-scale expression analysis
12. The regulating and epigenetic landscapes of genomes in mammals. Epigenetic modification of genomes and their functional and structural implications
13. RNA analysis. Arrays and sequencing technologies. Non-encoding RNA in mammals. The role of microRNA
14. The ENCODE project. In-depth functional knowledge of the genome
Genome dynamics.
15. Mutation. Mutation, innovation and disease. Mutation in the context of current genomic projects
16. Mutations under environmental stress: radiation and chemical mutagens
17. Recombination (I). Linkage disequilibrium and its measures. Diploid and haploid genetic Information. Genome phasing.
18. Recombination (II). Chromosome recombination. Recombination hotspots: detection and causes. Differences between species and populations
19. The HapMap project and its implications for the study of diversity and on genetics of complex traits. High performance genotyping technologies
20. My genome: lessons from individual genomes. JCV, JDW, NA18507, YH, and the 1000genome Project. Implications for personalised medicine
21. Structural reorganisations. Variation in the number of copies and segmental duplications. Implications for health
Genomes and phenotypes.
22. Genes, genomes and disease. The genetic base of complex traits. Genome-wide association studies.
23. Inheritability. Quantitative genetics and quantitative trait loci. The genomics of cancer and the use of genome biology. Pharmacogenomics
24. The genetic base of complex adaptations. Detection of natural selection in the genome. Positive selection or adaptation. Purifying selection measures
How genomes evolve.
25. Origins and early evolution of genomes. Size and complexity
26. Acquisition of new genes. Gene and genome duplications
27. Molecular phylogenetics
28. Old genomes. The Neanderthal genome project and its implications
Other activities
Seminars and poster
Each student must prepare a study to present in poster format on a very specific subject: sequencing a genome. There will be seminars beforehand on the work that needs to be done, the working tools to be used and how the presentation should be made. The tools used in research, both for obtaining the sequence and analysis, will be discussed in these seminars.
Each work will discuss: "what we have learnt with the genome sequence..." about a specific species, about a specific strain, about a specific individual, about a range of species, about an ecosystem.
The work must be presented as a poster written in English, and everyone must give a short explanation of it.
4. Assessment
The assessment will consist of four aspects:
1. Multiple choice questions in the general termly test. Factual knowledge will be emphasised. These account for 35% of the final mark.
2. Short essay questions, assessing the capacity for reasoning and integration of the knowledge acquired and accounting for 35% of the final mark.
3. Assessment of the poster production work, assessment of the poster and the explanation, accounting for 30% of the final mark.
4. Formative evolution. There will be a formative evaluation test halfway through the term. If passed, a bonus will be added to the final mark, which will increase on a linear basis from 0.25 (mark of 5) to 0.5 (mark of 10).
5. Bibliography and teaching resources
5.1. Basic bibliography
6. Methodology
7. Programme of activities