SASA14001U Quantitative Genomics, Breeding and Systems Biology
MSc Programme in Animal Science - semi-compulsory
The goal of this course is to teach advanced topics and engage students in practical aspects of quantitative genetics, genomic breeding and integrative genomic and systems biology methods, using high-throughput –omics datasets, complex phenotypes and pedigrees in animals, plants and humans. Research, innovation and development in modern life, biological, health and medical sciences are virtually impossible without quantitative- or statistical genomics and integrative systems biology methods. While the course is targeting Animal Science MSc students, it is relevant for MSc and PhD students specializing in human and plant genetics as well as biotechnology, bio-medicine and bioinformatics. It is expected to provide a strong foundation for students to either pursue PhD degrees and/or to provide essential qualifications and skills that are highly demanded in the in the agri-biotech, life and genomic science, bio-statistical, bio-medical industries and breeding industry. Initially, the quantitative genetic theory will be introduced for single and multiple loci including mutation, migration, selection, linkage (dis)equilibrium, genetic parameters, and response to selection. Different inheritance models and principles of estimation of heritability and prediction of breeding values of animals from various information sources such as phenotypic information, pedigree and single nucleotide polymorphisms (ie. SNPs) will be covered. Basic principles of linkage mapping, Quantitative Trait Loci (QTL) analysis and candidate gene analyses will be covered. Genome-wide association studies (GWAS) using SNP genetic markers and principles of genomic breeding values and genomic selection will be introduced with some hands-on experience using livestock and/or companion animal genome datasets. Basic principles of microarray or next generation based RNAseq or transcriptomic data and other –omic data analyses to discover causal and regulatory genes and biomarkers for common diseases and traits will be covered, with example experimental datasets. Concepts of integrated genomics or systems-genetics approaches as well as systems biology will be covered. Students will be introduced to some statistical and systems genetics and bioinformatic software to do these genome analyses. Current hot topics will be discussed in journal clubs, where also classical keynote publications are treated. Students will use one or more of the presented methodologies to analyze three to four research problem sets to gain working experience in this field.
After completing the course students should be able to
participate in designing quantitative or population-based genetic
or genomic studies, transcriptomic (gene expression) experiments
and perform linkage or QTL mapping, GWAS, and prediction of
(genomic) breeding values. Students should also have some basic
knowledge and skills to perform integrative systems genetics /
systems biology analyses using large volumes of multiple data types
such as high throughput genomic and transcriptomic datasets in
animals, humans and plants. More specifically, they should:
Knowledge:
- have a comprehensive understanding of the quantitative- and
population genetics, GWAS, genomic (animal) breeding theory and
designing breeding plans.
- have a basic understanding of statistical and systems
genetics approaches involved in detecting genes and
biomarkers with large (causal and regulatory) effects on complex
diseases and various traits
Skills:
- be able to use advanced methods in estimating genetic parameters
in populations and conduct GWAS using genomic, phenotytpic and
pedigree datasets
- be able to apply methods to predict (genomic) breeding values
- be able to write own computer programs or use readily available
software packages to perform relevant analyses
- be able to design systems biology, genomic and
transcriptomic experiments, analyse data and interpret results
related to gene and biomarker discovery for complex diseases and
traits in animals and other species
Competencies:
- be able to transfer knowledge and skills gained during the course
to solve new issues or challenges posed by the research and
innovation community including quantitative genomics, systems
genetics and breeding experiments and be able publish results
- be able to design/contribute to gene and biomarker discovery
experiments in animals, humans and other organisms
- be able to specify relevant research problems in mammalian
genomics and analyse them
- be able to critically discuss research results and compare with
literature findings
- Falconer D.S. & Mackay T.F.C. (1996) Introduction to
quantitative genetics, 4th ed, Longman, England
- R.A. Mrode. (2005). Linear models for the prediction of animal
breeding values, 2nd ed, CABI Publishing
- Genome-Wide Association Studies and Genomic Prediction. Editors:
Cedric Gondro, Julius van der Werf and Ben Hayes. Series: Methods
in Molecular Biology, Vol. 1019
ISBN 978-1-62703-447-0, 2013, XI, 566 pages, Humana Press
(Available as both e-Book and Hard cover)
- Various handouts (e.g. notes on genomic-wide association tests,
genomic selection, gene expression data and systems genetics
analyses) and scientific papers
LBIF10184U Molecular Genetics
SBIF10170U Mammalian Genomics
- Category
- Hours
- Colloquia
- 20
- Exam
- 1
- Lectures
- 50
- Practical exercises
- 110
- Preparation
- 100
- Project work
- 131
- Total
- 412
- Credit
- 15 ECTS
- Type of assessment
- Oral examination, 40 minutesThe oral examination is at the end of the course and consists of two parts (equal weights). Firstly, students will be asked questions on any one of the topics covered in the course (random draw). Secondly, students draw a specific topic to present followed by discussion. The possible topics for part 2 are known to the students in advance. The oral examination can last up to 40 minutes (total for both parts). Students get 45 minutes to prepare the oral exam
- Aid
- Only certain aids allowed
All aids allowed for preparation
Some Aid allowed during examination:
- Project, presentation and own notes - Marking scale
- 7-point grading scale
- Censorship form
- No external censorship
Internal examiner
Criteria for exam assesment
For the first part of the oral exam, students should be able to answer questions regarding key concepts (both theoretical and experimental aspects of the entire course) and demonstrate good knowledge and understanding of the learned subject areas.
For the second part of the oral exam, students, via their oral presentation, should demonstrate thorough understanding of the specific topic or a mini-project presented and be able to answer questions regarding the specific topic or mini-project.
Course information
- Language
- English
- Course code
- SASA14001U
- Credit
- 15 ECTS
- Level
- Full Degree Master
- Duration
- 1 block
- Placement
- Block 2
- Schedule
- A And B
- Course capacity
- No limit
- Continuing and further education
- Study board
- The Study Board for Veterinary Medicine and Animal Science
Contracting department
- Department of Veterinary Clinical and Animal Sciences
Course responsibles
- Haja Kadarmideen
Biology and Biotechnology, Bio-statistics