Cancer Genomics Workshop

Date:

 Monday 30 June Friday 4 July 2014

Venue: 

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

Application opens: 

Friday 05 January 2018

Participation: 

Open application with selection

Contact: 

Johanna Langrish

Registration fee: 

£725

Registration closed

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Overview

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. Lectures will give insight into bioinformatics concepts required to analyze cancer genomic data. Practicals will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of cancer genomics data under the guidance of the lecturers and teaching assistants.

The course covers data analysis of cancer genomics data.
Topics will include:

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.

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.

Syllabus, tools and resources

This course covers:

  • An ntroduction to cancer genomics
  • Visualisation of cancer genome features
  • Analytical methods to detect somatic mutations
  • Genome rearrangements and copy number alterations
  • RNA-seq data analysis
  • pathway and network analysis in cancer genomics

Programme

Time Topic Trainer
Day 1 - Monday 30 June 2014
12:00 - 13:00 Lunch  
13:00 - 14:00 Course introduction Gabriella Rustici
14:00 - 15:30 Lecture: Introduction to next generation sequencing Louis Letourneau & Mathieu  Bourgey
15:30 - 15:45 Tea/coffee break  
15:45 - 17:30 Lecture: Introduction to cancer genomics and its caveats Tobias Rausch
19:00 Dinner at Hinxton Hall  
Day 2 - Tuesday 01 July 2014
08:30 - 09:30 Lecture: SNV, Clonality and purity analysis Louis Letourneau & Mathieu Bourgey
09:30 - 10:30 Lecture: Copy Number Variation (CNV) analysis (WGS and SNParray) Louis Letourneau & Mathieu  Bourgey
10:30 - 11:00 Tea/coffee break  
11:00 - 12:00 Practical: data processing, alignment, Single Nucleotide Variants (SNV) calling Louis Letourneau & Mathieu  Bourgey
12:00 - 13:00 Lunch  
13:00 - 15:00 Practical: data processing, alignment, SNV calling Louis Letourneau & Mathieu Bourgey
15:00 - 15:15 Tea/coffee break  
15:15 - 16:15 Lecture: Structural Variants (SV) analysis Tobias Rausch
16:15 - 18:00 Practical: SV analysis Tobias Rausch
19:00 Dinner at Hinxton Hall  
Day 3 - Wednesday 02 July 2014
08:30 - 09:30 Lecture: Submitting data to EGA Jeff Almeida-King
09:30 - 10:30 Lecture: Validation and exploratory analysis Louis Letourneau & Mathieu  Bourgey
10:30 - 11:00 Tea/coffee break
11:00 - 12:00 Practical: CNV analysis Louis Letourneau & Mathieu  Bourgey
12:00 - 13:00 Lunch  
13:00 - 15:00 Practical: CNV + exploratory analysis of cancer data + free analysis Louis Letourneau & Mathieu Bourgey
15:00 - 15:30 Tea/coffee break  
15:30 - 17:30 Practical: exploratory analysis of cancer data + free analysis (cont.) Louis Letourneau & Mathieu Bourgey
17:30 - 18:30 Lecture/Practical: COSMIC - the world's knowledge of somatic mutations in human cancer Simon Forbes
19:30 Dinner at Hinxton Hall  
     
Day 4 - Thursday 03 July 2014
09:00 - 10:00 Lecture: Introduction to RNA-seq, with an overview of common research questions Liliana Greger
10:00 - 10:30 Lecture: Dealing with raw data: QA + filtering Liliana Greger
10:30 - 10:45 Tea/coffee break  
10:45 - 12:00 Practical: Dealing with raw data Liliana Greger & Mitra Barzine 
12:00 - 13:00 Lunch  
13:00 - 14:00 Lecture: Dealing with aligned data: mapping, expression estimation, normalisation Mitra Barzine
14:00 - 15:00 Practical: Dealing with aligned data Liliana Greger & Mitra Barzine
15:00 - 15:15 Tea/coffee break
15:15 - 17:30 Practical: Dealing with aligned data Liliana Greger & Mitra Barzine
19:00 College Dinner in Cambridge  
Day 5 - Friday 04 July 2014
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 & Gabriella Rustici
12:00 - 13:00 Lunch
13:00 - 14:00 Lecture: Mining for combinatorial patterns of mutations in large-scale cancer genomics data sets Francesco Iorio
14:00 - 15:00 Practical: Tools for the identification of mutual exclusively mutated network modules Francesco Iorio 
15:00 - 15:15 Tea/coffee break
15:15 - 17:30 Practical: Tools for therapeutic biomarker discovery - GDSC and DoRothEA Francesco Iorio
17:30 Feedback