CMBS2404 Sequencing technologies now and in the future (2–5 cr)

Sequencing is a biological method that allows the determination of the exact order of nucleotides, the basic units of DNA and RNA, in DNA or RNA molecules. This process is central to genetics and molecular biology, as it enables the understanding and research of the genetic makeup of organisms. Sequencing techniques have evolved over the years. The field has moved from original Sanger sequencing to modern methods such as Next-Generation Sequencing (NGS), which allows for the rapid and cost-effective sequencing of large amounts of DNA or RNA. These techniques have revolutionized genetics, enabling new medical breakthroughs such as personalized medicine. Sequencing technologies are widely used in research, development, and quality control.

The course divides into two parts, lectures (2 op) and practical laboratory work (3 op).

The learning goals for lectures are the following:

1. Milestones in sequencing technology - from Sanger sequencing to Next-Generation Sequencing (NGS)

2. Principles of sequencing DNA and RNA

3. Current Sequencing Technologies: Illumina, PacBio, and Oxford Nanopore

4. Comparison of sequencing methodologies

5. Applications of Current Sequencing Technologies: Genomics and medical research, metagenomics, environmental studies, epidemiology and agriculture

6. Overview of sequencing data analysis pipeline, bioinformatics tools and databases

7. Ethical Considerations in Genetic Sequencing: privacy, consent, and data sharing in genomic research

8. Emerging Trends and Future Directions: Next Frontiers in Sequencing Technologies, single-cell sequencing, long-read sequencing advancements, AI and machine learning in sequencing data interpretation

9. Future of sequencing: Impact on, for example, personalized medicine, epidemiology, disease prevention and treatment

For laboratory part, the learning goals are the following:

Understanding DNA Isolation Techniques:

1. Learn the fundamental principles and techniques of DNA extraction from various sample types.

2. Gain hands-on experience in preparing samples for DNA isolation.

3. Develop the ability to critically assess the purity and concentration of isolated DNA.

Amplicon 16S Library Preparation:

1. Understand the significance of the 16S rRNA gene in microbial identification and phylogenetic studies.

2. Learn the steps involved in amplifying the 16S rRNA gene region using PCR.

3. Gain proficiency in preparing amplicon libraries, including primer selection, PCR setup, and amplicon purification.

Skills in Whole Genome Library Preparation:

1. Understand the process of library preparation for whole genome sequencing.

Quality Control and Validation:

1. Learn techniques for assessing the quality of prepared libraries using methods such as gel electrophoresis.

Basic analysis of the sequence data (more elaborated bioinformatic analysis are taught on ECOS1200)

The course divides into two parts, lectures (2 op) and practical laboratory work (3 op). The lecture-part must be completed before attending to the laboratory work.

The Laboratory part of the course is available to those who have completed the BIO Bachelors program and students in the Cellular and molecular biology and Nanoscience Masters programs. Part of the biological material used in the laboratory part comes from the course CMBS2405. Respectively, the data produced during the laboratory part are utilized in the course ECOS1200 Advanced bioinformatics: microbial communities and genomes. However, it is not mandatory to attend these other courses. 

Understanding of fundamental biological structures and concepts, such as the structure and function of cells, DNA and RNA, and their roles within cells. A basic knowledge of genetics is also good to have. 

For laboratory work, previous experience in laboratory is required.

Lecture slides and articles on the topic.

All materials for the laboratory part will be given during the course.