Cancer Genomics

Date:

 Tuesday 20 Friday 23 June 2017

Venue: 

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

Application opens: 

Thursday February 02 2017

Application deadline: 

Friday March 31 2017

Participation: 

Open application with selection

Contact: 

Johanna Langrish

Registration fee: 

£500 (Including Accommodation)

Registration closed

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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 - Tuesday 20 June 2017
08:30 - 09:00 Registration  
09:00 - 09:30 Course introduction Gabriella Rustici 
09:30 - 10:30 Lecture: Introduction to high-throughput sequencing and its application in cancer  Mathieu Bourgey
10:30 - 10:45 Tea/Coffee Break  
10:45 - 12:30 Lecture: Introduction to cancer genomics and its caveats  Tobias Rausch
12:30 - 13:30 Lunch  
13:30 - 14:30 Lecture: RNA-seq analysis  Myrto Kostadima
14:30 - 15:30 Practical: RNA-seq analysis  Myrto Kostadima
15:30 - 15:45 Tea/Coffee Break
15:45 - 18:00 Practical: RNA-seq analysis Myrto Kostadima 
19:00 Evening meal at Hinxton Hall  
Day 2 - Wednesday 21 June 2017
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 - 18:00 Practical: SV analysis Tobias Rausch
19:00 Evening meal at Hinxton Hall   
Day 3 - Thursday 22 June 2017 
08:30 - 09:30 Lecture: CNV analysis using NGS Data   
09:30 - 10:30 Practical: CNV analysis - deletion/amplification, calling CNVs, visualisation, interpretation Mathieu Bourgey
10:30 - 10:45 Tea/Coffee Break   
10:45 - 13:00 Practical: CNV analysis - deletion/amplification, calling CNVs, visualisation, interpretation Mathieu Bourgey
13:00 - 14:00 Lunch  
14:00 - 15:30 Practical: Data visualization Mathieu Bourgey 
15:30 - 15:45 Tea/Coffee Break   
15:45 - 18:00 Practical: Data visualization Mathieu Bourgey 
19:00 Evening meal at the Red Lion Pub, Hinxton  
Day 4 - Friday 23 June 2017
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