Virtual course

Cancer genomics (Virtual)

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 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.

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

Trainers

Ajay Mishra
EMBL-EBI, UK
Moritz Gerstung
EMBL-EBI, UK
Robert Eveleigh
McGill University, Canada
Tobias Rausch
EMBL, Heidelberg, Germany
Wendi Bacon
EMBL-EBI, UK
Alexey Larionov
Cancer Research UK Cambridge Institute
Francesco Iorio
Wellcome Sanger Institute, UK
Mathieu Bourgey
McGill University and Genome Quebec Innovation Centre, Canada

Programme

Day 1 – Monday 06 July 2020
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 High Throughput Sequencing and its Application in Cancer (Lecture Recap and Live Q&A Session)  Mathieu Bourgey 
12:15-14:00 Break  
14:00-15:00 Introduction to cancer genomics and its caveats (Lecture Recap and Live Q&A Session)  Tobias Rausch
15:00-15:15 Break  
15:15-15:45 Cancer epigenetics and whole-genome haplotyping (Lecture Recap and Live Q&A Session)  Tobias Rausch
15:45-16:45 Networking/Poster session All
16:45 End of the day  
Day 2 – Tuesday 30 June 2020
09:45-10:00 Morning challenge  All
10:00-10:45 Structural Variation (Lecture Recap and Live Q&A)  Tobias Rausch
10:45-11:00 break  
11:00-11:30 SNV Analysis (Lecture recap and Live Q&A)  Mathieu Bourgey 
11:30-12:30 Variant Annotation, Filtration and Visualisation (Practical Demonstration)  Robert Eveleigh
12:30-13:30 Break  
13:30-14:15 Variant Annotation, Filtration and Visualisation (Troubleshooting)  Robert Eveleigh
14:15 Quick comfort break    
14:15-15:15 Variant Annotation, Filtration and Visualisation (Troubleshooting)  Robert Eveleigh
15:15-16:15 Networking/Poster session All
16:15 End of the day  
Day 3 – Wednesday 01 July 2020
09:45-10:00 Morning challenge  All
10:00-11:25 Copy Number Variation (CNV) Analysis Using NGS data (Lecture Recap and Live Q&A Session)  Mathieu Bourgey 
11:25-11:30 Break  
11:30-12:15 CNV Analysis: Deletion/Amplification, Calling CNVs, Visualisation, Interpretation  Robert Eveleigh
12:15-13:05 Lunch  
13:05-14:05 CNV Analysis: Deletion/Amplification, Calling CNVs, Visualisation, Interpretation  Robert Eveleigh
14:05-14:15 Tea/coffee break  
14:15-15:15 Data Visualisation (Practical Demonstration and Troubleshooting)  Robert Eveleigh
15:15-16:16 Networking/Poster session All
16:15 End of the day  
Day 4 – Thursday 02 July 2020
09:45-10:00 Morning challenge  All
10:00-10:45 CRISPR-Cas9 Genome Editing for Identifying Cancer Dependencies and New Therapeutic Targets (Lecture Recap and Live Q&A Session)  Francesco Iorio
10:45-11:00 Break  
11:00-12:00 Pre-processing, QC Assessment and Visualization of Gene Essentiality Profiles from CRISPR-Cas9 Screens (Practicals and Troubleshooting)  Francesco Iorio
12:00-13:00 Break  
13:00-13:45 RNA-seq Analysis (Lecture Recap and Live Q&A Session)  Alexey Lorionov
13:45-14:00 Break  
14:00-15:00 RNA-seq Analysis (Practicals and Troubleshooting)  Alexey Lorionov
15:00-16:00 Networking/Poster Presentation  All
16:00 End of the day  
Day 5 – Friday 03 July 2020
9:30-10:45   Single Cell Transcriptomics  Wendi Bacon
10:45-11:00 Break  
11:00-12:30 Single Cell Transcriptomics continued  Wendi Bacon
11:45-12:45 Single cell approaches/keynote To be confirmed
12:30-13:00 Course wrap-up and feedback Ajay Mishra
13:00 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 which will also ask you to:
    • Provide three short paragraphs with a biography, work history and description of your current research interests; each paragraph should be no more than 100 words
    • Upload 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 online by 23:59 GMT on Friday 13 March, 2020.

Incomplete applications will not be considered.

This course has ended

06 - 10 July 2020
Free
Contact
Rebecca Nicholl

Organisers
  • Ajay Mishra
    EMBL-EBI, UK
  • Moritz Gerstung
    EMBL-EBI, UK

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