Print Syllabus

Syllabus

BK0003 Genome analysis, 15.0 Credits

Genomanalys

Subjects

Bioinformatics

Education cycle

Master’s level

Modules

Title	Credits	Code
Laboratory project	5.0	0101
Computer exercises	3.0	0102
Group discussions	3.0	0103
Written and oral examination	4.0	0104

Advanced study in the main field

Second cycle, has only first-cycle course/s as entry requirements
Master’s level (A1N)

Grading scale

Language

English

Prior knowledge

180 credits and

60 credits within one of following main field of study: biology, animal science, equine science, veterinary nursing, veterinary medicine, agricultural science, forestry science, food science, medicine, bio medicine, nursing practice, biomedical laboratory science, bio technology, computer science, mathematics or chemistry and

5 credits cell biology or 5 credits genetics or 5 credits biochemistry and

English 6

Objectives

The course intends to provide advanced knowledge of methods for studies of eukaryotic genomes, including their organization and evolution. There is a focus on animal genomics, but methodological and theoretical aspects of the course are applicable on many different organisms.

Upon successful completion of the course, students will be able to

• in detail describe structure, diversity and evolution of eukaryotic genomes and genes,
• in detail describe various types of genetic variation,
• in detail explain state of the art and large-scale methods to analyze genetic variation (eg. whole genome sequencing), and gene expression analysis (eg. RNA-seq),
• apply and critically process basic molecular phylogenetic / -genomic and evolutionary analysis,
• in detail describe the different types of RNA in the transcriptome and their function,
• describe principles for transcriptional regulation,
• describe and plan different approaches for functional analysis of genes and genomes,
• summarize genetic recombination and its applications within genome analysis,
• summarize and evaluate the principles of whole genome mapping and comparative genomics to identify genes and loci underlying mendelian and quantitative inherited diseases as well as important phenotypic traits,
• explain epigenetic and epigenomic markers and methods for the analysis of these,
• explain the concept of genome editing and transgenic animals,
• compile data and apply basic statistics relevant to genome analysis,
• use and evaluate molecular genetic laboratory methods and basic bioinformatics methods.

Content

Subject-related content

The contents build largely on animal genome research. Both laboratory and theoretical teaching is for the most part directly applicable also within eg. human or plant genetics. The course is based on current state-of-the-art methodology and research.

Computer exercises and group discussions will cover:

• molecular evolution and phylogenetics/-genomics,
• genetic variation, sequence analysis and primer design,
• gene mapping and genomewide association analysis,
• QTL analysis,
• whole genome sequencing,
• epigenetics/-genomics,
• copy-number variation analysis.

The aim of the computer exercises is to give the students useful tools for basic genetic and genomic analyses. Therefore the computer exercises use free and open source software that the student can download to their own laptop.

Teaching formats

To further student learning and promote discussion, a variety of methods are used: lectures, exercises, project work, discussions and laboratory sessions.

The course focuses on the following generic competencies

Oral and written communication, problem solving and critical thinking.

The following components are compulsory

Exercises and laboratory sessions.

Grading form

The grade requirements within the course grading system are set out in specific criteria. These criteria must be available by the course start at the latest.

Formats and requirements for examination

Passed written and oral examination. Approved participation in compulsory components.

• If a student has failed an examination, the examiner has the right to issue supplementary assignments. This applies if it is possible and there are grounds to do so.

• The examiner can provide an adapted assessment to students entitled to study support for students with disabilities following a decision by the university. Examiners may also issue an adapted examination or provide an alternative way for the students to take the exam.

• If this syllabus is withdrawn, SLU may introduce transitional provisions for examining students admitted based on this syllabus and who have not yet passed the course.

• For the assessment of an independent project (degree project), the examiner may also allow a student to add supplemental information after the deadline for submission. Read more in the Education Planning and Administration Handbook.

Other information

• The right to participate in teaching and/or supervision only applies for the course instance the student was admitted to and registered on.

• If there are special reasons, students are entitled to participate in components with compulsory attendance when the course is given again. Read more in the Education Planning and Administration Handbook.

Responsible department

Department of Animal Biosciences