Cancer Genomics Workshop
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Date:
Monday 30 June - Friday 4 July 2014Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Friday 05 January 2018Participation:
Open application with selectionContact:
Johanna LangrishRegistration fee:
£725Registration closed
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 | |