NNEK22001U Metabolomics

Volume 2022/2023
Education

MSc Programme in Biochemistry

MSc Programme in Biology

Content

Description

Metabolomics is a powerful tool in nutrition, biology, pharmaceutical and clinical research, since it allows the understanding of metabolic pathways, the early diagnosis of diseases, the development and the evaluation of effective therapies or diets.

Lectures will start with an introduction to the human and microbial metabolism, and with an overview of metabolomics used in the discovery of new predictive biomarkers, the investigation of metabolic pathways in nutritional and other diseases, toxicology and personalized medicine. The course will cover the use of both untargeted and targeted metabolomics approaches and will provide details on each step of the metabolomics pipeline:

 

  • Study design and sample collection with particular focus on human studies, including related ethical and data safety issues.
  • Sample treatment and instrumental methods (NMR, GC-MS, LC-MS), with a particular focus on LC-MS.
  • Data pre-processing, uni- and multi-variate statistical data analysis with R (using a LC-MS dataset).
  • Identification of metabolites through MS spectral interpretation and biomarkers validation.

 

The course will include both theoretical lectures and practical exercises on the different steps of the metabolomics pipeline. Moreover, the students will work on a group project in which they will either perform a human intervention study (consumption of one or two different foods among the students themselves, collection of biological samples, sample preparation and analysis) for the identification of intake biomarkers, or they will work on datasets from pre-existing human studies.

Learning Outcome

Objectives

The main objectives of the course is 1) to provide an overview of the scientific possibilities opened by metabolomics in different fields, and 2) to introduce the prerequisites and the key methods for conducting a human metabolomics study. The course is recommended for students who want to know how to work with explorative as well as targeted metabolomics, especially for including this technology in human and animal studies at universities and/or companies in the food and pharma areas.

At the end of the course, students are expected to have the following:

Knowledge:

  • Outline the human and microbiota metabolism.
  • Outline the different applications of metabolomics.
  • Bullet-point the applications of other -omics fields.
  • Bullet-point the applications of metabolomics for in vitro and in vivo studies.
  • Define and interpret different study designs for human studies.
  • Define the ethical and data safety issues associated with human studies.
  • Define different sample collection and preparation methods in metabolomics.
  • Define different analytical instrumental techniques applied in metabolomics.
  • Define different data preprocessing tools and statistical analysis methods applied in metabolomics.
  • Interpret LC-MS data.
  • Define different biomarker validation methods.

 

Skills:

  • Prepare a draft protocol for conducting an experimental human study including the steps to recruit subjects.
  • Choose the appropriate design for conducting a specific human study that aims to include metabolomics.
  • Choose the appropriate sample preparation and instrumental method for a human study.
  • Choose an appropriate data treatment strategy and statistical data analysis approach.
  • Perform basic experimental procedures for sample preparation in the lab.
  • Perform data treatment and preprocessing.
  • Perform statistical data analysis with R.
  • Perform identification of metabolites through MS spectral interpretation.
  • Write a report about a metabolomics project.
  • Present the metabolomics project in class.
  • Giving peer feedback to the other students.

 

Competences:

  • Critically assess metabolomics studies based on the quality of the study design, analytical method, statistical analysis method and identification.
  • Critically assess the suitability of a human study design for metabolomics analysis.
  • Critically assess the results of statistical data analysis and how data treatment affects these results.
  • Critically assess the results of metabolite identification from a metabolic perspective.
  • Solve clinical and nutritional questions by integrating knowledge and skills from chemistry, biology, biochemistry, statistics, nutrition, health and ethics.
  • Work together in a team on a joint metabolomics project.

Course literature will be announced at study start and during the course on the course page at Absalon.

Academic qualifications equivalent to a BSc degree is recommended.
The theoretical part will consist of a mixture of lectures and exercises. Due to the interdisciplinarity of the course, pre-recorded lectures will be provided to students lacking in basic concepts for pre-course training. The practical part will consist in a voluntary participation of the students in a human study to analyze their own samples by metabolomics – alternatively they will receive a dataset comprising of anonymized data.
  • Category
  • Hours
  • Lectures
  • 32
  • Preparation
  • 104
  • Practical exercises
  • 14
  • Laboratory
  • 10
  • Project work
  • 44
  • Exam
  • 2
  • Total
  • 206
Continuous feedback during the course of the semester
Credit
7,5 ECTS
Type of assessment
Oral examination, 30 min
Type of assessment details
The exam will consist of an individual oral examination of 30 minutes, without preparation time.
The exam questions will be based on the group work and report associated with the group work as well as on the topics discussed in class throughout the course.
Exam registration requirements

In order to participate to the exam it is mandatory to participate in the group work (metabolomics group project) and to provide written and oral presentations of the group work in class.

Aid
Without aids
Marking scale
7-point grading scale
Censorship form
No external censorship
Two assessors.
Re-exam

The re-exam will consist of an oral examination of 30 minutes, without preparation time. 
Both the topics of the course and the content of the group work will be discussed and evaluated.  

Exam registration requirements must be fullfilled no later than 3 weeks before the reexamination.

Criteria for exam assesment

See "Intended learning outcome".