SASA14001U  Quantitative Genomics, Breeding and Systems Biology

Volume 2015/2016
Education

MSc Programme in Animal Science - semi-compulsory

Content

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.

Learning Outcome

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

LMAF10070U Statistical Data Analysis 2
LBIF10184U Molecular Genetics
SBIF10170U Mammalian Genomics
Lectures, theoretical exercises, practical computer exercises, journal club, excursions and self study.
Credit
15 ECTS
Type of assessment
Oral examination, 40 minutes
The 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.

  • Category
  • Hours
  • Lectures
  • 50
  • Practical exercises
  • 110
  • Preparation
  • 100
  • Exam
  • 1
  • Colloquia
  • 20
  • Project work
  • 131
  • Total
  • 412