Cancer Genomics


 Monday 17 Thursday 20 June 2019


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

Application opens: 

Wednesday 19 December 2018

Application deadline: 

Friday 22 March 2019


Open application with selection


Marina Pujol

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 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.



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 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