Virtual course

Cancer genomics

Welcome to the new EMBL-EBI Training site. Please tell us what you think!

This course will focus on the analysis of data from genomic studies of cancer.  Lectures and interactive sessions will give an insight into the bioinformatic concepts required to analyse such data, whilst practical sessions will enable the participants to apply statistical methods to the analysis of cancer genomics data under the guidance of the lecturers.

Virtual course

The course will involve participants learning via pre-recorded lectures, live presentations, and trainer Q&A sessions. The content will be delivered over Zoom, with additional text communication over Slack.

Computational practicals will be run on EMBL-EBI's virtual training infrastructure; this means there is no need to have a powerful computer to run exercises or a requirement to install complex software before the course. Trainers will be available to provide support, answer questions, and further explain the analysis during these practicals.

Participants will need to be available between the hours of 09:30-18:00 BST each day of the course.

Who is this course for?

This course is aimed at advanced PhD students and post-doctoral researchers who are applying or planning to apply high throughput sequencing technologies in cancer research and wish to familiarise themselves with bioinformatics tools and data analysis methodologies specific to cancer data.

Familiarity with the technology and biological use cases of high throughput sequencing is required, as is some experience with R/Bioconductor (basic understanding of the R syntax and ability to manipulate R objects) and the Unix/Linux operating system.

What will I learn?

Learning outcomes

After this course you should be able to:

  • Evaluate the applications and challenges of HTS in the study of cancer genomics
  • Detect, visualise and annotate copy number variation
  • Interpret complex genomic rearrangements such as structural variants
  • Indicate the principles of tumour purity, heterogeneity and evolution and how these influence/impact upon bioinformatics analysis
  • Perform alignment and quantification of expression of RNA-seq datasets
Course content

During this course you will learn about:

  • Application of high throughput sequencing (HTS) in cancer
  • Introduction to cancer genomics and epigenetics
  • Structural variation, SNV and CNV analysis and data visualisation
  • Application of CRISPR-Cas9 genome editing in studying cancer
  • RNA-seq analysis


Ajay Mishra
Moritz Gerstung
Robert Eveleigh
McGill University, Canada
Tobias Rausch
EMBL, Heidelberg, Germany
Alexey Larionov
Medical Genetics Department, University of Cambridge, UK
Francesco Iorio
Wellcome Sanger Institute, UK
Mathieu Bourgey
McGill University and Genome Quebec Innovation Centre, Canada
Aurélie Ernst
DKFZ, Heidelberg, Germany
Ana Cvejic
Department of Haematology, University of Cambridge, UK



Day 1 – Monday 17 May 2021 (time in BST)  
10:00-10:30 EMBL-EBI introduction Ajay Mishra
10:30-11:00 Course introduction Moritz Gerstung
11:00-11:15 Break  
11:15-12:15 Introduction to cancer genomics and its caveats (Lecture recap and live Q&A session)  Tobias Rausch 
12:15-14:00 Break  
14:00-15:00 Introduction to high throughput sequencing and its application in cancer (lecture recap and live Q&A session)  Mathieu Bourgey
15:00-15:15 Break  
15:15-16:15 Cancer epigenetics and whole-genome haplotyping Tobias Rausch
16:15-16:30 Break  
16:30-17:30 Flash talks All
17:30 End of the day  
Day 2 – Tuesday 18 May 2021 (time in BST)  
09:45-10:00 Morning challenge  All
10:00-11:00 Structural variation Tobias Rausch
11:00-11:15 break  
11:15-12:15 Flash talks All
12:15-13:00 Break  
13:00-14:15 SNV analysis  Mathieu Bourgey 
14:15-14:30 Break  
14:30-15:30 Introduction to DNA-Seq processing for cancer data - SNVs (Practical) Robert Eveleigh
15:30-15:45 Break  
15:45-16:45 Variant data interpretation and visualisation (Practical) Robert Eveleigh
16:45-17:00 Break  
17:00-18:00 Practical troubleshooting session  Robert Eveleigh
18:00 End of the day  
Day 3 – Wednesday 19 May 2021 (time in BST)  
09:45-10:00 Morning challenge  All
10:00-11:00 Keynote lecture Aurélie Ernst
11:00-11:15 Break  
11:15-12:15 Flash talks All
12:15-13:15 Break  
13:15-14:30 Copy Number Variation (CNV) analysis using NGS data Mathieu Bourgey 
14:30-14:45 Break  
14:45-15:45 CNV analysis: Deletion/amplification, calling CNVs, visualisation, interpretation  Robert Eveleigh
15:45-16:00 Break  
16:00-17:00 CNV analysis: Deletion/amplification, calling CNVs, visualisation, interpretation  Robert Eveleigh
17:00-17:10 Break  
17:10-18:00 Data visualisation (Practical demonstration and troubleshooting)  Robert Eveleigh
18:00 End of the day  
Day 4 – Thursday 20 May 2021 (time in BST)  
09:45-10:00 Morning challenge  All
10:00-11:15 CRISPR-Cas9 genome editing for identifying cancer dependencies and new therapeutic targets Francesco Iorio
11:15-11:30 Break  
11:30-12:30 Pre-processing, QC assessment and visualization of gene essentiality profiles from CRISPR-Cas9 screens (practicals and troubleshooting)  Francesco Iorio
12:30-13:30 Break  
13:30-14:30 Flash talks All
14:30-14:45 Break  
14:45-16:00 Short-read RNA-seq analysis Alexey Larionov
16:00-16:15 Break  
16:15-17:30 Short-read RNA-seq analysis (practicals and troubleshooting)  Alexey Larionov
17:30 End of the day  
Day 5 – Friday 21 May 2021 (time in BST)  
09:45-10:00 Morning challenge   
10:00-11:00   Long-read RNA-seq analysis Alexey Larionov
11:00-11:15 Break  
11:15-12:15 Long-read RNA-seq analysis  Alexey Larionov
12:15-13:00 Break  
13:00-14:00 Single cell approaches (keynote lecture) Ana Cvejic
14:00-14:30 Course wrap-up and feedback Ajay Mishra
14:30 End of the course  

Please read our page on application advice before starting your application. In order to be considered for a place on this course, you must do the following:

  • Complete the online application form providing answers as directed
  • Ensure you add relevant information to the "Application submission" section where you are asked to provide three 300-word paragraphs that cover your:
    • scientific biography
    • work history
    • current research interests
  • Upload a letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course

Please submit all documents during the application process by midnight on Friday 26 Feb 2021. 

Incomplete applications will not be considered.

All applicants will be informed of the status of their application (successful, waiting list, rejected) by Friday 12 March 2021. If you have any questions regarding the application process please contact Jane Reynolds at


Participant flash talks

All participants will be asked to give a short presentation about their research work as part of the course. These provide an opportunity to share their research with the other participants and provide a forum for discussion. Further details will be provided if you are accepted for this course.


This course has ended

17 - 21 May 2021
Jane Reynolds

  • Ajay Mishra
  • Moritz Gerstung

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