Course at EMBL-EBI

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 will give an insight into the bioinformatic concepts required to analyze 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 and teaching assistants.

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


Tobias Rausch
EMBL Heidelberg, Germany
Moritz Gerstung
Alexey Larionov
Cancer Research UK Cambridge Institute, UK
Francesco Iorio
Wellcome Sanger Institute, UK
Mathieu Bourgey
McGill University and Genome Quebec Innovation Centre, Canada
Wendi Bacon
Yuanhua Huang


Day 1 – Monday 17 June 2019
08:30-09:00 Arrival, registration and coffee  
09:00-09:30 Course introduction Anna Swan & Moritz Gerstung
09:30-11:00 Lecture: Introduction to high-throughput sequencing and its application in cancer Mathieu Bourgey
11:00-11:15 Break  
11:15-12:45 Lecture: Introduction to cancer genomics and its caveats Tobias Rausch
12:45-13:30 Lunch  
13:30-14:30 Lecture: SNV analysis Mathieu Bourgey
14:30-15:30 Practical: Variant annotation, filtration and visualisation Mathieu Bourgey
15:30-15:45 Break  
15:45-18:00 Practical: Variant annotation, filtration and visualisation Mathieu Bourgey
18:00 End of day  
19:00 Evening meal  
Day 2 – Tuesday 18 June 2019
09:00-10:00 Lecture: Cancer Epigenetics and Whole-Genome Haplotyping Tobias Rausch
10:00-11:00 Lecture: SV analysis Tobias Rausch
11:00-11:15 Break  
11:15-13:00 Practical: SV analysis Tobias Rausch
13:00-14:00 Lunch  
14:00-15:30 Lecture: CNV analysis using NGS data Mathieu Bourgey
15:30-15:45 Break  
15:45-18:00 CNV analysis - deletion/amplification, calling CNVs, visualisation, interpretation Mathieu Bourgey
18:00 End of day  
19:00 Evening meal  
Day 3 – Wednesday 19 June 2019
09:00-10:30 Practical: Data visualisation Mathieu Bourgey
10:30-10:45 Break  
10:45-12:30 Data visualisation Mathieu Bourgey
12:30-13:30 Lunch  
13:30-14:30 CRISPR-Cas9 genome editing for identifying cancer dependencies and new therapeutic targets Francesco Iorio
14:30-15:00 Break  
15:00-17:00 Pre-processing, QC assessment and visualization of gene essentiality profiles from CRISPR-Cas9 screens Francesco Iorio
18:00 End of day  
19:00 Evening meal  
Day 4 – Thursday 20 June 2019
09:00-10:00 Lecture: RNA-Seq analysis  Alexey Larionov
10:00-10:30 Break  
10:30-12:00 Practical: RNA-Seq analysis  Alexey Larionov
12:00-13:00 Lunch  
13:00-14:30 Single-cell transcriptomics: Overview & challenges Wendi Bacon
14:30-15:00 Break  
15:00-16:00 Single-cell approaches Yuanhua Huang
16:00-16:15 Course wrap-up and feedback Anna Swan
16:15 End of course  
16:30 Shuttle to Cambridge Train Station  

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:

  1. Complete the online application form
  2. Provide a Microsoft Word (.docx) document containing three short paragraphs with a biography, work history and description of your current research interests; each paragraph should be no more than 100 words
  3. Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course

Please submit all documents to Marina Pujol ( by 12:00 GMT on Friday 22 March, 2019.

Incomplete applications will not be considered.

Accommodation will be provided in the Wellcome Genome Campus Conference Centre Monday-Thursday inclusive. Please contact the Conference Centre directly if you wish to arrange to stay additional nights. The course fee includes breakfast and evening meals at Hinxton Hall, as well as breaks and lunches outside the EMBL-EBI training rooms.

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17 - 20 June 2019
European Bioinformatics Institute United Kingdom
Marina Pujol

  • Sarah Morgan
  • Moritz Gerstung
  • Anna Swan

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