NBIK15013U  Genome Sequence Analysis

Volume 2017/2018
Education

MSc Programme in Biochemistry
MSc Programme in Biology
MSc Programme in Molecular Biomedicine
MSc Programme in Biology-Biotechnology

Content

The course focuses on second-generation sequencing technology, its wide applications, and the Bioinformatics analysis of produced sequencing data. Newer sequencing technology (third generation) will also be overviewed. Strategies for analyzing second generation sequencing data will be covered, including quality control of raw sequencing data, mapping reads to a reference genome and contemporary downstream data analyses. Downstream analyses will include gene/transcript expression quantification and de novo transcript reconstruction from RNA sequencing data and variant/genotype calling from whole-genome DNA sequencing data. 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:

  • Second generation sequencing technology
    • Library construction (theoretical level)
    • Sequencing by synthesis
    • Bridge amplification
    • Base calling
    • Newer developments (third generation)
  • Applications of second generation sequencing technology
    • Overview of how second generation sequencing can be used / adapted to answer various biological questions
    • Whole-genome DNA sequencing
    • RNA sequencing
  • Analysis strategies and workflows for second generation sequencing data
    • Filtering and quality evaluation of raw reads
    • Mapping of sequencing reads onto a reference genome
    • Sequencing coverage
    • Variant and genotype calling
    • Gene/transcript expression quantification and de novo transcript reconstruction from RNA sequencing data
  • Basic knowledge of the various statistical/​computational approaches and tools used when dealing with sequencing data and how and why these differ between sequencing applications
  • Familiarity with of state-of-the-art statistical and computational approaches for dealing with whole-genome sequencing data for variant calling and RNA-sequencing data for gene transcript expression quantification
  • Basic knowledge of the issues and potential problems with second generation sequencing data and how to deal with those
  • Genomic annotation of sequencing data and genome browsers
     

Skills:

  • Identify differentially expression of gene transcripts between biological samples of different types or conditions
  • Identify mutations in an experimental sample by variant calling
  • Design and carry out genetic experiments to relate identified variants with mutant phenotypes


Competences:

  • Critically evaluate results of second generation sequencing experiments from different perspectives (molecular biology, bioinformatics, genetics)
  • Independently analyze and interpret whole-genome DNA sequencing data and RNA-sequencing data

Notes, articles.
See Absalon.

BSc in Biology, Biochemistry, Molecular Biomedicine or equivalent.
Lectures, theoretical and practical exercises, colloquia.
Written
Oral
Individual
Collective
Continuous feedback during the course of the semester
Peer feedback (Students give each other feedback)
Credit
7,5 ECTS
Type of assessment
Continuous assessment
Participation in the theoretical and practical exercises and colloquia.
The course uses continuous assessment with five different assignments. Students will work on each assignment in groups and present their results in written or oral form in group or individually, depending on the assignment. The assignments are weighted with the following percentages: 10%, 20%, 20%, 20%, 30%, for assignments 1, 2, 3, 4, 5, respectively.
Aid
All aids allowed
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.

  • Category
  • Hours
  • Preparation
  • 131
  • Theory exercises
  • 21
  • Practical exercises
  • 42
  • Colloquia
  • 12
  • Total
  • 206