Methods: omics in biomedical research
BIOENG-519 / 4 credits
Teacher(s): Chrast Roman, Garcia Miguel, Guex Nicolas Jean Philippe, Iseli Christian, Mangeat Bastien, Pavlou Maria, Pojer Florence
Language: English
Withdrawal: It is not allowed to withdraw from this subject after the registration deadline.
Summary
High-throughput methodologies broadly called Omics allow to characterize the complexity and dynamics of any biological system. This course will provide a general description of different methods related to the Omics field followed by hands-on rotations in participating technological platforms.
Content
During the initial part of the course we will provide a general description of different methods related to the "omics" field. The presented techniques will be discussed in terms of their rationale, applicability and limitations. During the second part of the course, students will take part in hands-on rotations in participating technological platforms allowing them to put the theory into practice inside a laboratory environment.
The following topics will be covered during the theoretical and practical parts of the course:
General introduction to Omics
From genes to proteins
- Strategy of cloning for protein expression, production of proteins in different cellular settings.
- Purification of proteins by diverse methods.
- Quantity and quality controls of final protein samples by biophysical techniques.
Flow cytometry and cell sorting
- Basics of flow cytometry and cytometer subsystems.
- Principles of Multicolour flow cytometry including fluorescence and fluorochromes and appropriate experimental controls.
- Principles on cell sorting: why and how, technological principle, basic parts of a cell sorter.
Genomics and transcriptomics
Broad overview of genomics/transcriptomics techniques to investigate, at bulk and single cell levels:
- Gene expression (RNA-seq, qPCR).
- Epigenetic control of gene expression (ChIP-seq, ATAC-seq).
- Spatial organization of gene expression (spatial transcriptomics).
Proteomics
- Introduction to proteomics and mass spectrometry.
- Mass spectrometry-based proteomics workflows.
- Data analysis (search engines and databases, statistics, data visualization and result interpretation).
Bioinformatics
- Experimental design and sample nomenclature.
- Data clustering and its applications: theory and practice.
- Data formats and handling.
- Data quality control, analysis and visualization, mapping on reference genomes.
- Variant calling, peak calling, quantification, GSEA.
- Protein and transcript reference databases, nomenclature.
- Biological function knowledge, domains, structures, annotations and visualization.
- Evaluation of genetic mutation impact.
Keywords
Omics (including single cell omics)
Bioinformatics
Quality control
Data analysis
Data interpretation
Learning Prerequisites
Required courses
Learning Outcomes
By the end of the course, the student must be able to:
- Choose appropriate Omics technique(s) to design relevant experiment
- Apply the concept of data quality control
- Interpret the generated data
- Contextualise theoretical and technical concepts of the covered Omics techniques
Transversal skills
- Use a work methodology appropriate to the task.
- Collect data.
- Plan and carry out activities in a way which makes optimal use of available time and other resources.
- Evaluate one's own performance in the team, receive and respond appropriately to feedback.
Teaching methods
3 weeks of common theoretical lectures
11 weeks of practical rotation sessions in small groups in scientific platforms: Protein Production and Structure, Flow Cytometry, Gene Expression, Proteomics and Bioinformatics.
Expected student activities
In-person attendance is expected for all practical rotation sessions
Lectures
Hands-on practical work during practical rotation sessions in scientific platforms
Reading articles
Project presentation
Assessment methods
Written reports or oral presentations for rotation sessions during the semester.
Written exam during exam session.
Supervision
| Office hours | Yes |
| Assistants | Yes |
| Forum | No |
Resources
Websites
- https://www.epfl.ch/research/facilities/ptpsp/
- https://www.epfl.ch/research/facilities/cytometry/
- https://www.epfl.ch/research/facilities/gene-expression-core-facility/
- https://www.epfl.ch/research/facilities/proteomics-core-facility/
- https://www.epfl.ch/research/facilities/ptbicc/
Moodle Link
In the programs
- Semester: Fall
- Number of places: 24
- Exam form: Written (winter session)
- Subject examined: Methods: omics in biomedical research
- Courses: 1 Hour(s) per week x 14 weeks
- TP: 3 Hour(s) per week x 14 weeks
- Type: optional
- Semester: Fall
- Number of places: 24
- Exam form: Written (winter session)
- Subject examined: Methods: omics in biomedical research
- Courses: 1 Hour(s) per week x 14 weeks
- TP: 3 Hour(s) per week x 14 weeks
- Type: optional