NBIK15013U Genome Sequence Analysis

Volume 2015/2016
Education

MSc Programme in Biochemistry
MSc Programme in Biology
MSc Programme in Molecular Biomedicine

Content

The course will introduce contemporary methods for analyzing whole genome sequnecing (WGS) data generated by next generation sequencing (NGS) platforms. The theoretical framework for DNA shearing, linker addition, immobilization and solid-phase amplification will be explained. Algorithms for mapping sequence reads onto a reference model genome (yeast) will be covered. Based on authentic biological samples, mutants will be identified by variant calling. Genetic experiments that relate the identified mutants to a biological phenotype will be conducted.

Learning Outcome

Knowledge:

  • Next generation sequencing techniques
  • Statistics of sequencing coverage
  • Methods for mapping of sequencing runs onto a reference genome
  • Variant calling algorithms
  • Relationship between phenotypic and genotypic segregation

 

Skills:

  • Design experiment to map mutations by whole genome sequencing
  • Analyse, interpret and critically evaluate WGS data
  • Map WGS data onto a reference genome
  • Identify mutations in an experimental sample by variant calling
  • Design genetic experiments to relate identified variants with mutants phenotypes

 

Competences:

  • The students will be able to critically evaluate resultas of WGS experiments from different perspectives (molecular biology, bioinformatics, genetics)
Literature

Notes, articles, biological material. See Absalon

BSc in Biology, Bioinformatics, Biochemistry, Molecular Biomedicine or equivalent.
Theoretical and practical exercises, colloquia.
  • Category
  • Hours
  • Colloquia
  • 12
  • Practical exercises
  • 42
  • Preparation
  • 131
  • Theory exercises
  • 21
  • Total
  • 206
Credit
7,5 ECTS
Type of assessment
Continuous assessment
Participation in the theoretical and practical exercises and colloquia.
Exam registration requirements

Participation in 80% of the exercises is mandatory.
If the requirement is not fulfilled, the student must take the course again the next year.

Marking scale
passed/not passed
Censorship form
No external censorship
One internal examiner
Re-exam

The reexam will be held as an oral exam (30 minutes) with 1 hour preparation time (all aids allowed).

Criteria for exam assesment

See Learning Outcome.