Clinical Cancer Genomics

Doctoral course within the doctoral programme in FoTO
Course number: 5534
Credit points: 1.5

Learning outcomes

At the end of this course the student will be able to:

  • show a basic insight into the cancer genome.
  • understand how the cancer genome can be interrogated through tissues and liquid biopsies.
  • understand how to apply technology to obtain relevant information from the cancer genome.
  • understand the file formats used in high throughput sequencing.
  • use the command line and running bioinformatic tools.
  • understand the constituents of a bioinformatics pipeline for processing Illumina sequencing data and to run such a pipeline.
  • perform quality control on DNA- and RNA sequencing data for cancer sequencing purposes.
  • call somatic- and germline variation.
  • curate somatic- and germline variation for a clinical setting.
  • annotate somatic- and germline variation.
  • visualise data in R.
  • use online resources such as genome browsers and portals for variant annotation.

Contents of the course

This course aims to provide an introduction to cancer genomics and to support to obtain practical knowledge regarding 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 facilitate that students get an understanding of basic theory and obtain practical knowledge that will enable course participants to apply the covered methodologies in their own research- or clinical laboratory.

Course director and contact person

Johan Lindberg

Principal researcher

Gunilla Nilsson Roos

Educational administrator