Functional Genomics Theory, 7.5 Credits

Contents

The course provides technical insight and understanding of methods utilised to perform functional genomics studies. The concept of functional genomics is introduced and a key component of the course is developing an understanding of how the methods introduced can be combined in studies aiming to identify the function of genes and how a genome functions. Topics covered include methods to sequence genome, assay gene, metabolite and protein abundance and to profile epigenetic modifications. Concepts in data quality control and statistical analysis are introduced. Integrative approaches to understanding gene function and associating genes or genomic polymorphisms to phenotypes are explained, including systems genetics and co-expression network analyses. The course includes details of methods for validation studies in addition to considering potential ethical implications of the knowledge obtained from functional genomics studies.

Expected learning outcomes

Upon completion of the course, students should be able to:

1. Summarise the historical background of methods used to assay gene expression, comparing these to currently employed technologies.
2. Explain the purpose of functional genomics, demonstrate uses of a functional genomics approach and evaluate the challenges faced in assigning function to genes.
3. Explain and apply the technologic principles of currently utilised methods within the field of functional genomics.
4. Integrate genomic, epigenetic and external effects in the context of understanding gene and genome function.
5. Appraise and select relevant methods used in functional genomics studies, comparing their relative strengths, weaknesses and associated analysis challenges.
6. Design an experiment to elucidate and validate the function of unknown genes, including selection, evaluation and justification of associated technical methods and approaches and their associated analysis and visualisation.
7. Evaluate the suitability of integrative approaches including systems biology, systems genetics, genome wide association studies and co-expression network analysis.
8. Assess the ethical implications arising from implementation of functional genomics approaches or knowledge, including prediction of near-term future effects.

Required Knowledge

90 ECTS credits including courses in genetics 15 ECTS credits, molecular genetics 15 ECTS credits, as well as immunology or plant cell and molecular biology 15 ECTS credits. Swedish for basic eligibility for higher education programmes and English B/6. Requirements for Swedish only apply if the course is held in Swedish.

Form of instruction

The course consists of lectures, flipped class room sessions (where students watch pre-recorded lectures and discuss these during dedicated teaching time), group discussion and debate sessions and student-led learning sessions to revise course content. There are two computer lab sessions to provide hands-on experience of processing and analysing sequencing and gene expression data.

Literature
There is no textbook for this course. Relevant literature is provided during the course including links to further reading for each lecture and specific papers to be used for group discussion sessions. Links to other media, including lecture and conference videos and information resources are provided as required.
 

Examination modes

Modes of assessmentThe ELOs will be assessed using
Student led course content revision sessions, paper discussions and debates. Students will present a summary of research papers assigned as group reading exercises, debate ethical issues and contribute to student-led content revision sessions. Each session is graded U/G on the basis of individual short reflective texts. A G grade in all is required. If a student fails any component(s), this will be re-examined in an oral exam between the student and the course examiner. (ELOs 3,4,8). A final summary grade of G/U will be awarded for this component of the course, with a G requiring a G grade for all graded sessions.
Short written summary of computer lab session results. Graded U/G. (ELO 3).
Final hall exam consisting of short answer questions to test knowledge of specific ELOs (10 questions) and two long answer essay questions to test understanding and integration across ELOs. Each short answer question is marked as G or U (ELOs 1,2,3,6,7) and the short answer section is graded VG - 7+ passes, G - 5+ passes or U - fewer than 5 Gs. Each long-answer essay question is graded as VG, G or U (ELOs 2,3,4,5,7). A single grade for the exam is then determined as VG) 2+VG, G) any other combination of VG/G, U) U in any component.
 
The final course grade is determined when all examined components have been completed. The final course grade will be based on all examined components. For engineers: 5) 2+xVG; 4) 1+xVG; 3) 3xG, U) for U in any component; Others VG) 2+VG, G) any other combination of VG/G, and U) for U in any component.
 
The grading system will be introduced and discussed in the first course lecture. During this lecture the course will also be placed within the context of the national goals for an advanced level course.
 
Course Evaluation 
If any of the examined components are assigned Fail (U), the final course grade will be assigned as Fail (U) until the failed component has been passed. Only failed component(s) must be re-examined.
 
Students who received a pass grade may not retake that assessed component.
 
Students who do not pass the regular examination arranged can take a re-examination in accordance with the Umeå University Regulations for tests and examinations at the undergraduate and graduate level (FS 1.1.2-553-14). The first re-examination will be offered no later than two months after the first examination, except where an ordinary examination takes place in May or June, in which case a first re-examination will be offered within three months after the first examination. In addition, at least one additional re-examination will be offered within one year of regular examination.
 
In cases where the examination cannot be repeated under the current rules for re-examination, the exam will be replaced with an alternative. The scope and content of such information should not be disproportionate to the missed examination.
 
A student who has taken two examinations in a course, or part of a course, has the right to have another examiner appointed unless there are specific reasons against it (6 ch. 22, § HF). Requests for new-examiners should be addressed to the head of the Department of Plant Physiology.
 
In the event that the curriculum expires or major changes are made, a student is assured at least three examination opportunities (including the regular examination) based on the syllabus at taken by the student over a period of a maximum of two years from the date of the syllabus change.