Cancer Genomics

Date:

 Monday 27 June - Friday 1 July 2016

Venue: 

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

Application opens: 

Friday 19 February 2016

Application deadline: 

Friday 01 April 2016

Participation: 

Open application with selection

Contact: 

Johanna Langrish

Registration fee: 

£750

Registration closed

Overview

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.

Audience

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.

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
  • Understand the principles of tumour purity, heterogeneity and evolution and how this influences / impacts upon bioinformatics analysis
  • Perform alignment and quantification of expression of RNA-seq datasets
  • Explore network deregulation in cancer

Programme

Time Topic Trainer
Day 1 - Monday 27th June 2016
12:00 - 13:00 Lunch and Registration 
13:00 - 14:00 Course introduction   Gabriella Rustici   
14:00 - 15:30 Lecture: Introduction to high-throughput sequencing and its application in cancer Mathieu Bourgey 
15:30 - 15:45 Tea/coffee break 
15:45 - 17:30 Lecture: Introduction to cancer genomics and it's caveats   Tobias Rausch 
19:00 Evening meal at Hinxton Hall 
Day 2 - Tuesday 28th June 2016
08:30 - 09:30 Lecture: SNV analysis  Mathieu Bourgey 
09:30 - 10:30  Practical: variant annotation, filtration and visualization Mathieu Bourgey
10:30 - 10:45 Tea/coffee break 
10:45 - 12:30  Practical: variant annotation, filtration and visualization Mathieu Bourgey
12:30 - 13:30  Lunch  
13:30 - 14:30  Lecture: SV analysis Tobias Rausch 
14:30 - 15:30  Lecture: Single-Molecule Sequencing and Whole-Genome Haplotyping
Tobias Rausch 
15:30 - 15:45  Tea/coffee break   
15:45 - 18:30  Practical: SV analysis Tobias Rausch 
19:00 Evening meal at Hinxton Hall 
Day 3 - Wednesday 29th June 2016
08:30 - 09:30  Lecture: CNV analysis using NGS data  Mathieu Bourgey   
09:30 - 10:30  Practical: CNV analysis – deletion/amplification, calling CNVs, visualisation, interpretation Mathieu Bourgey   
10:30 - 10:45  Tea/Coffee break     
10:45 - 12:30  Practical: CNV analysis – deletion/amplification, calling CNVs, visualisation, interpretation Mathieu Bourgey   
12:30 - 13:30  Lunch   
13:30 - 15:30  Practical: Data visualization Mathieu Bourgey 
15:30 - 15:45 Tea/coffee break    
15:45 - 17:00 Practical: Data visualization Mathieu Bourgey
17:00 - 18:00 Lecture/Practical: COSMIC - the world's knowledge of somatic mutations in humar cancer  Simon Forbes
19:00 Evening meal at Hinxton Hall   
Day 4 - Thursday 30th June 2016
08:30 - 09:30 Lecture: Methylation analysis in cancer Yaseen Assenov
09:30 - 10:30 Practical: Methylation analysis in cancer Yaseen Assenov
10:30 - 10:45 Tea/coffee break   
10:45 - 13:00 Practical: Methylation analysis in cancer Yaseen Assenov
13:00 - 14:00 Lunch   
14:00 - 15:00 Lecture: RNA-seq analysis in cancer Tibor Nagy
15:00 - 15:30 Practical: RNA-seq analysis in cancer
Tibor Nagy
15:30 - 15:45 Tea/coffee break   
15:45 - 17:00 Practical: RNA-seq analysis in cancer Tibor Nagy
17:00 - 19:00 Free time  
19:00 Evening meal at Red Lion Pub, Hinxton
 
     
Day 5 - Friday 1st July 2016
09:00 - 10:00 Lecture: From genomes to networks  Francesco Iorio 
10:00 - 10:30 Tea/coffee break  
10:30 - 12:00 Practical: From genomes to networks   Francesco Iorio 
12:00 - 13:00 Lunch   
13:00 - 14:00 Lecture: Mining for combinatorial patterns of mutations in large-scale cancer genomic data sets  Francesco Iorio 
14:00 - 15:00 Lecture: Tools for the identification of mutual exclusively mutated network modules  Francesco Iorio 
15:00 - 15:15 Tea/coffee break - Feedback Survey  
15:15 - 17:30 Practical: Tools for therapeutic biomaker discovery - GDSC and DoRothEA  Francesco Iorio
17:45 End of the course and departures - Coach leaves for Cambridge Train Station at 17:45
  
European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

At EMBL-EBI, we manage the world’s public biological data and make it freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. Set on the beautiful Wellcome Genome Campus near Cambridge in the UK, we support scientists throughout the world in seeking solutions to challenges in healthcare, agriculture and the environment.

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In association with

How to apply

In order to be considered for a place on this course applicants must do the following:

  1. Complete the online application form.
  2. Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course.

Further details will be provided on your confirmation email after completing the online form.

Incomplete applications will NOT be considered. Please read through the following guidance document for more information on how to complete your application.

Application deadline

01 April 2016

Number of places

30 places

Registration closed

Organisers

EMBL-EBI Training Team

Gabriella Rustici - University of Cambridge, UK

Trainers

Gabriella Rustici - University of Cambridge, UK

Mathieu Bourgey - McGill University and Genome Quebec Innovation Centre

Tobias Rausch - EMBL

Francesco Iorio - EMBL-EBI, UK

Simon Forbes - Wellcome Sanger Institute

Materials & attachments

Course materials