Course at EMBL-EBI

Cancer genomics and transcriptomics

This course will focus on the analysis of data from genomic studies of cancer. It will also highlight the application of transcriptomic analysis and single-cell technologies in cancer. Talks 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 trainers.

In-person course

We plan to deliver this course in an in-person manner onsite at our training suite at EMBL-EBI, Hinxton.  Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing.

Who is this course for?

We welcome applications from PhD students, post-doc researchers, and those working in industry. This course is well-suited for those who are applying, or planning to apply, high throughput sequencing and single-cell 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 (HTS) 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.

If you are not already familiar with these then please ensure that you complete these free tutorials before you attend the course:

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
  • Explain the principles of tumour purity, heterogeneity and evolution, and how we detect or quantify them using bioinformatic approaches
  • Explore the application of CRISPR-Cas9 genome editing in cancer studies
  • Perform alignment and quantification of expression of RNA-seq datasets
  • Explore the application of single-cell sequencing in cancer studies
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 (both short and long reads)
  • Single-cell research in cancer


Isidro Cortes Ciriano
Francesco Iorio
Human Technopole
Alexey Larionov
Cranfield University
Ajay Mishra
Tobias Rausch


The programme below is subjected to minor changes

Day/Time Topic Trainer
Day one – Monday 10 July 2023
09:00  09:30 Arrival and registration  
09:30  09:45 Welcome Ajay Mishra
09:45  10:45 Course introduction Isidro Cortes-Ciriano
10:45  11:00 Break  
11:00  12:30 Introduction to cancer genomics and its caveats Tobias Rausch
12:30  13:30 Lunch  
13:30  14:30 High-throughput sequencing and single-nucleotide variant analysis in cancer Tobias Rausch and Isidro Cortes-Ciriano lab
14:30  15:00 Break  
15:00  17:30 Practical: alignment, quality control, and SNV analysis Tobias Rausch and Isidro Cortes-Ciriano lab
17:30 End of day  
18:30 Dinner  
Day two – Tuesday 11 July 2023
09:30  10:30 Structural and copy-number variation analysis Tobias Rausch and Isidro Cortes-Ciriano lab
10:30  11:00 Break  
11:00  12:00 Interrogating cancer genomes using long-reads Tobias Rausch and Isidro Cortes-Ciriano lab
12:00  13:00 Lunch  
13:00  15:00 Practicals: SV/CNV analysis using short-reads Tobias Rausch and Isidro Cortes-Ciriano lab
15:00  15:30 Break  
15:30  18:00 Practicals: long-read cancer genome analysis Tobias Rausch and Isidro Cortes-Ciriano lab
18:00 End of day  
18:30 Dinner  
Day three – Wednesday 12 July 2023
09:30  10:30 Introduction to single cell technologies in cancer genomics TBC
10:30  11:00 Break  
11:00  12:00 Single-cell data analysis Tobias Rausch and Isidro Cortes-Ciriano lab
12:00  13:00 Lunch  
13:00  15:00 Practical: single cell genomics TBC
15:00  16:00 Coffee break and poster session  
16:00  18:00 Practical: single-cell genomics TBC
18:00 End of day  
18:30 Dinner  
Day four – Thursday 13 July 2023
09:30  10:30 CRISPR-Cas9 genome editing for identifying cancer dependencies, and new therapeutic targets Francesco Iorio
10:30  10:45 Break  
10:45  12:30 Pre-processing, QC assessment, and visualisation of gene essentiality profiles from CRISPR-Cas9 screens (practicals and troubleshooting) Francesco Iorio
12:30  13:30 Lunch  
13:30  15:00 Short-read RNA-seq analysis Alexey Larionov
15:00  16:00 Coffee break and poster session  
16:00  18:00 Short-read RNA-seq analysis (practicals and troubleshooting) Alexey Larionov
18:00 End of day  
18:30 Dinner  
Day five – Friday 14 July 2023
09:30  10:30 Long-read RNA-seq analysis Alexey Larionov
10:30  10:45 Break  
10:45  12:15 Long-read RNA-seq analysis (practicals and troubleshooting) Alexey Larionov
12:15  13:00 Lunch  
14:40  15:00 Course wrap-up and feedback Ajay Mishra
15:00 End of course  
15:30 Coach to Cambridge train station  

Please read our page on application support 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.
  • Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
    • pre-requisite skills and knowledge
    • current work and course expectations
    • data availability
  • Upload one 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 23:59 on 9 April 2023. Items marked * in the application are mandatory. Incomplete registrations will not be processed. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 24 April 2023. If you have any questions regarding the application process please contact Sophie Spencer.

The registration fee of £825.00 includes:

  • Catering as detailed on the course programme
  • Accommodation for four nights (10, 11, 12, and 13 July)
  • Bespoke course handbook with links to all course materials
  • Use of a computer in the EMBL-EBI training suite throughout the course
  • Shuttle bus on the final course day to Cambridge train station 


Hotel rooms will be provided onsite at Hinxton Hall Conference Centre. Please contact them directly if you wish to arrange to stay additional nights around the course dates.


The course includes catering as detailed on the programme tab. Successful applicants will be asked for any dietary requirements and allergies upon registration. 

Course materials

The course materials from the 2022 edition of the course are now live and available for you to use. They provide a mixture of pre-recorded lectures, presentations, and practicals from the course, and will give you a snapshot of what to expect in the 2023 edition.


All participants are expected to present a poster that will be displayed during the course outside the training room. Successful applicants will be asked to submit their poster upon registration. We will print these for you and have them available when you arrive on site.

All posters should:

•         be A2 in size 420mm x 594 mm
•         be in a portrait orientation
•         include your photograph and contact information

We expect the posters to act as a talking point between you, other participants and the trainers on the course. The posters will be displayed throughout the week so people can view them during breaks and lunch. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the gathered participants.


Applications close
09 April 2023

10 - 14 July 2023
European Bioinformatics Institute United Kingdom
£825.00 inclusive of four nights accommodation and catering, including dinner
Sophie Spencer
Open application with selection
30 places

  • Isidro Cortes Ciriano
  • Ajay Mishra
  • Tobias Rausch

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