Course description
This course aims to provide an introduction cancer genomics and practical knowledge how to apply state of the art methodology to interrogate the cancer genome in a routine clinical setting or a clinical trial setting. The course will include lectures covering the technology advancements that have enabled high-throughput analysis of cancer genomes and the knowledge that can be obtained by applying these technologies. This encompasses both laboratory sample processing and downstream bioinformatics. Lectures will be held in the mornings with computer-based exercises in the afternoon. The exercises will include processing and analysis of DNA- and RNA-sequencing data covering file formats, quality control aspects, identification of somatic variation, curation of identified somatic- and germline variants for clinical use, clonality estimation and annotation of variants.
The main objective of the course is to provide basic theory and practical knowledge that will enable course participants to apply the covered methodologies in their own research- or clinical laboratory.
Requirements and Selection
Prerequisite courses, or equivalent
We expect each course participant to have basic Linux/Unix skills and to be able to run commands (programs) using a command-line interpreter or a shell terminal as available in Unix-like operating systems.
If you don’t currently know how to do this, but would like to take part in the course, we recommend checking out online resources such as https://scicomp.aalto.fi/scicomp/shell/ or this two-hour online introduction: https://www.hpc2n.umu.se/events/courses/2024/fall/intro-linux.
Selection
Selection will be based on:
1) the relevance of the course syllabus for the applicant’s doctoral project (according to written motivation).
2) start date of doctoral studies (priority given to earlier start date).
Course director
Johan Lindberg
Course syllabus
C8F6039
Department
Department of Medical Epidemiology and Biostatistics
Doctoral programme
Tumour Biology and Oncology (FoTO)
Type of course
**Other course
Keywords
cancer genomics, bioinformatics, cancer, sequencing