Cancer Genomics
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Date:
Tuesday 20 - Friday 23 June 2017Venue:
European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Thursday 02 February 2017Application deadline:
Friday 31 March 2017Participation:
Open application with selectionContact:
Johanna LangrishRegistration fee:
£500 (Including Accommodation)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 - 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 | |