4. High-throughput sequencing: Applications in cancer research
This one-week, full time course is aimed at PhD students in oncology with an interest in high throughput sequencing technology and its applications.
The course consists of lectures, computer exercises and discussions designed to provide the students with a basic understanding of what high-throughput sequencing is, what its applications are in basic and clinical cancer research, and how such sequencing data is analysed and interpreted.
Aims of the course
This course is designed to provide the students with a basic understanding of what high throughput sequencing is, what its applications are in basic and clinical cancer research, and how such sequencing data is analysed and interpreted.
The course will consist of lectures on sequencing technologies, DNA and RNA sequencing, as well as key concepts in data analysis such as quality control, commonly used file formats, data standards, and sequence alignment strategies.
These concepts will also be dealt with in computer exercises on basic command line and batch system usage, sequence alignments etc. Particular emphasis will be given to evaluation and critical assessment of findings from sequence data.
On completion of the course, students shall be able to:
- Explain basic principles behind high-throughput sequencing (HTS) technologies including the weaknesses and strengths of different approaches.
- Explain how HTS data can be used to study genetic variation, quantify gene expression, characterize gene and transcript structure, analyse gene regulation and assemble whole genomes.
- Explain the steps involved in common HTS data analyses such as sequence alignment, sequence variant detection, annotation and interpretation of functional variants, and data visualization.
- Explain the key concepts of alignment and de novo assembly.