Cancer Genomics

Date:

 Monday 18 Thursday 21 June 2018

Venue: 

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

Application opens: 

Thursday 05 January 2017

Application deadline: 

Friday 16 March 2018

Participation: 

Open application with selection

Registration fee: 

£530 (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
  • 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
  • Explore network deregulation in cancer

Programme

Time Topic Trainer
Day 1 - Monday 18 June 2018
08:30 - 09:00 Registration  
09:00 - 09:30 Course introduction Sarah Morgan / Moritz Gerstung
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 Rasuch
12:30 - 13:30 Lunch  
13:30 - 14:30 Lecture: SNV analysis Mathieu Bourgey
14:30 - 15:30 Practical: Variant annotation, filtration and visualization Mathieu Bourgey 
15:30 - 15:45 Tea/coffee break  
15:45 - 18:00 Practical: Variant annotation, filtration and visualization Mathieu Bourgey 
19:00 Evening meal at Hinxton Hall  
Day 2 - Tuesday 19 June 2018
08:30 - 09:30 Lecture: SV analysis Tobias Rausch
09:30 - 10:30 Lecture: Single-Molecule Sequencing and Whole-Genome Haplotyping Tobias Rausch
10:30 - 10:45 Tea/coffee break  
10:45 - 12:30 Practical: SV analysis Tobias Rausch
12:30 - 13:30 Lunch  
13:30 - 14:30 Lecture: CNV analysis using NGS Data Mathieu Bourgey
14:30 - 15:30 Practical: CNV analysis - deletion/amplification, calling CNVs, visualisation, interpretation Mathieu Bourgey
15:30 - 15:45 Tea/coffee break  
15:45 - 18:00 Practical: CNV analysis - deletion/amplification, calling CNVs, visualisation, interpretation Mathieu Bourgey
19:00 Evening meal at Hinxton Hall  
Day 3 - Wednesday 20 June 2018
09:00 - 10:30 Practical: Data visualization Mathieu Bourgey
10:30 - 10:45 Tea/coffee break  
10:45 - 12:30 Practical: Data visualization Mathieu Bourgey 
12:30 - 13:30 Lunch   
13:30 - 14:30 Lecture: RNA-Seq analysis Alexey Larionov

14:30 - 15:30

Practical: RNA-Seq analysis Alexey Larionov
15:30 - 15:45 Tea/coffee break  
15:45 - 18:00 Practical: RNA-Seq analysis Alexey Larionov
19:15 Evening meal at The Red Lion Pub, Hinxton  
Day 4 - Thursday 21 June 2018
09:00 - 10:00 Lecture: CRISPR-Cas9 genome editing for identifying cancer dependencies and new therapeutic targets Francesco Iorio
10:00 - 10:30 Tea/coffee break  
10:30 - 12:00 Practical: Pre-processing, QC assessment and visualization of gene essentiality profiles from CRISPR-Cas9 screens Francesco Iorio
12:00 - 13:00 Lunch  
13:00 - 14:30 Cancer genomics in the cloud Anmol Hemrom
14:30 - 15:00 Tea/coffee break  
15:00 - 16:00 Cancer genomics in the cloud Anmol Hemrom
16:00 - 16:30 Course wrap up and feedback Sarah Morgan
16:30 End of course and departures