Cancer genomics (Virtual)


 Monday 6 Friday 10 July 2020


European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Monday 09 December 2019

Application deadline: 

Friday 13 March 2020


Open application with selection


Rebecca Nicholl

Registration fee: 


Registration closed

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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 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 and teaching assistants.



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.


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

Additional information

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.


Day 1 – Monday 29 June 2020
09:30-10:00 Arrival, registration and tea/coffee  
10:00-10:30 EMBL-EBI introduction Ajay Mishra
10:30-11:00 Course introduction Moritz Gerstung
11:00-12:30 Introduction to high-throughput sequencing and its application in cancer Robert Eveleigh
12:30-13:30 Lunch  
13:30-15:00 Introduction to cancer genomics and its caveats Tobias Rausch
15:00-15:15 Tea/coffee break  
15:15-16:15 Lecture: Single-Nucleotide Polymorphism (SNV) Robert Eveleigh
16:15-17:15 Cancer epigenetics and whole-genome haplotyping Tobias Rausch
17:15 End of day  
18:30 Evening meal Hinxton Hall Restaurant
Day 2 – Tuesday 30 June 2020
09:00-10:30 Lecture on Structural Variation (SV)  Tobias Rausch
10:30-10:45 Tea/coffee break  
10:45-12:45 Practicals: SV analysis Tobias Rausch
12:45-13:30 Lunch  
13:30-15:00 Practicals: Variant annotation, filtration and visualisation Robert Eveleigh
15:00-15:15 Tea/coffee break  
15:15-17:15 Practicals: Variant annotation, filtration and visualisation (continued) Robert Eveleigh
17:15 End of the day  
18:30 Evening meal Red Lion, Hinxton
Day 3 – Wednesday 01 July 2020
09:30-10:30 Lecture: Copy Number Variation (CNV) analysis using NGS data Robert Eveleigh
10:30-10:45 Tea/coffee break  
10:45-12:45 CNV analysis: Deletion/amplification, calling CNVs, visualisation, interpretation Robert Eveleigh
12:45-13:30 Lunch  
13:30-15:15 Practicals: Data visualisation Robert Eveleigh
15:15-15:30 Tea/coffee break  
15:30-17:15 Practicals: Data visualisation (continued) Robert Eveleigh
17:15 End of the day  
18:00 Evening meal Hinxton Hall Restaurant
Day 4 – Thursday 02 July 2020
09:00-10:00 CRISPR-Cas9 genome editing for identifying cancer dependencies and new therapeutic targets Francesco Iorio
10:00-10:15 Tea/coffee break  
10:15-12:30 Pre-processing, QC assessment and visualization of gene essentiality profiles from CRISPR-Cas9 screens Francesco Iorio
12:30-13:30 Lunch  
13:30-15:00 Lecture: RNA-seq analysis Alexey Lorionov
15:00-15:15 Tea/coffee break  
15:15-17:15 Practicals: RNA-seq analysis Alexey Lorionov
17:15 End of the day  
18:00 Evening meal Hinxton Hall Restaurant
Day 5 – Friday 03 July 2020
09:00-10:00 Single cell transcriptomics: Overview and challenges Wendi Bacon
10:00-10:15 Tea/coffee break  
10:15-11:45 Single cell transcriptomics: Overview and challenges (continued) Wendi Bacon
11:45-12:45 Single cell approaches/keynote To be confirmed
12:45-13:00 Course wrap-up and feedback Ajay Mishra
13:00-14:00 Lunch  
14:15 Shuttle to Cambridge train station (stop5)