Course Objective1. The student has knowledge of essential methods in genomics and
understands the suitability and limitations of those methods, given a
scientific goal. These methods comprise: Genome mapping & sequencing,
Exome & RNA sequencing, Karyotyping, Comparative Genomic Hybridization,
Expression profiling with microarrays or ‘Gene Chips’, Proteomics,
Metabolomics, SNP arrays, non-invasive prenatal testing.
2. The student can identify and describe various types of genetic
variation within a natural population (SNPs, CNVs, repeats and other
types of genetic markers) and can derive the inheritance pattern of
genetic traits from a pedigree. He/she understands how the heritability
of a trait can be measured, how monogenetic disease genes can be
identified by haplotyping and linkage analysis, and how quantitative
trait loci and complex disease genes can be identified.
3. The student is familiar with the properties of important genetic
model organisms including yeast, nematodes, fruit flies and mice and can
choose the most suitable organism for a scientific problem. He/she can
explain how breeding strategies can be used to control genetic variation
and how these strategies can be applied in research.
4. The student is familiar with important methods for genetic
manipulation including transgenesis, homologous gene targeting, RNA
interference and genome editing and can write a research strategy
describing an effective approach for a given scientific aim.
5. The student can collect relevant information from public databases
(genome browsers, gene, transcript and protein sequence databases, 3D
structures, OMIM, PubMed) and apply the resulting information to solve
medical and biological problems.
6. The student can interpret genetic literature where the aforementioned
methods (see 1-4) are applied and present the key message to his/her
7. The student can reflect on the application of methods in medical
genomics in health care and discuss their potential impact on future
health care. Such applications include gene therapy, stem cell therapy,
drug design and development, clinical diagnostics and genetic
In the past decennia, large initiatives of the scientific community have
culminated in an essentially complete description of all our genetic
material, together called the genome. After this landmark, more and more
genomes have been analyzed. These include genomes of many other species,
allowing to recognize DNA sequences that are highly conserved through
evolution. In addition, the genomes of many different human individuals
can be compared to get an idea of the genetic variation that exists in
The term genomics refers to the discipline that studies an organism’s
entire genome, as opposed to studies that focus on one or few selected
genes. In this course, you will learn fundamental concepts relevant for
such studies and be introduced to powerful techniques that can be
applied to investigate all genes simultaneously (i.e. on a genome-wide
scale). The availability of such techniques is of immense value for
biomedical sciences, for example in clinical genetics where these
techniques can rapidly detect genetic abnormalities in patients. The
steeply increasing efficiency of mutation discovery prompts a new need
for bioinformatics tools to handle all the available data and to
distinguish causative mutations from neutral variations. At the same
time systematic approaches to restore genetic defects are also
progressing. In the coming years, genome-wide approaches can be expected
to yield many medical advancements, collectively referred to as medical
At the start of the course, a basic knowledge of molecular biology or
genetics is assumed. Key facts will be recapitulated in the chapter
“Molecular Biology Basics” for the purpose of memory refreshment. The
structural organization of the genome in prokaryotic and eukaryotic
organisms will be described.
Similarity comparisons between genomes from different species can yield
information about evolutionary changes and relate observations in
different organisms. This approach is referred to as “Comparative
Genomics”. Certain species have become model organisms in genomics
research; these will be introduced together with their individual
strengths and weaknesses.
To find relevant pieces of information in publicly available databases,
a proper use of similarity search algorithms is required. The most
important algortithms are BLAST or BLAT search tools. You will develop
skills in using these tools in various assignments. In addition,
analysis of the genome and its products requires many other special
tools and techniques. Methods are described to study the transcriptome
(in the form of mRNA), the proteome (in the form of proteins) and the
metabolome (in the form of chemical compounds made by enzymes).
When focusing on the human genome, powerful approaches have been
developed to identify the location and identity of disease genes.
Different modes of inheritance (e.g. Mendelian or complex)require
different approaches for successful disease gene finding. These
approaches are summarized in the chapters “Mendelian Genetics” and
“Complex Trait Genetics“.
For final confirmation of the causal involvement of a disease gene
mutation in an associated phenotype, genome manipulation is often
performed in model organisms (e.g. mice). The resulting animal model can
subsequently be used to study the disease’s pathogenesis and to develop
treatment options. In this context, it is also important to consider
ethical and legal aspects of genetic manipulation, working with
experimental animals, stem cell technology and other applications of
Teaching MethodsThe course comprises lectures (~40 h) and workgroups (~15 h). In
addition, approximately 120h of self study is expected. The lectures
(optional but highly recommended) will cover the complete theory
providing a basis for the many concepts and methods in medical genomics.
The workgroups (for which participation is obligatory) will emphasize
how these methods can be applied in health care or biomedical research.
Method of AssessmentThe final grade is composed of two parts. To pass for the course, both
parts must be completed with a 5.5 or higher. First, the full course
theory will be assessed by a multiple choice digital exam at the end of
the course. This test will contribute 60% to the final grade. Second,
the performance in workgroup assignments will collectively count for 40%
of the final grade. These assignments include oral presentations, groups
discussions and written assignments.
LiteratureA syllabus will be provided for the cost price at the first lecture of
the course. Unless indicated otherwize, all theory in the syllabus
belongs to the exam program. Exceptions will be explicitly announced via
Target AudienceOptional course for first-year BSc Biomedical Sciences
Custom Course RegistrationPlease sign in for this module via VUnet.
|Language of Tuition||English|
|Faculty||Faculty of Science|
|Course Coordinator||dr. ir. A.J.A. Groffen|
|Examiner||dr. ir. A.J.A. Groffen|
You need to register for this course yourself
Last-minute registration is available for this course.
|Teaching Methods||Study Group, Lecture, Computer lab|
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