CAGE-KID Cancer Genomics Workshop
Learning Objectives
Is it right for me?
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.
What will I learn?
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.
What will it cover?
The course covers data analysis of cancer genomics data.
Topics will include: introduction to cancer genomics; how to visualize 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.
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - 18 March 2013 - Materials |
||
| 09:00-10:30 | Talk: Introduction to cancer genomics | Louis Letourneau and Mathieu Bourgey |
| 10:30-10:45 | Coffee Break | |
| 10:45-12:00 | Talk: Introduction to Next-generation sequencing | Louis Letourneau and Mathieu Bourgey |
| 12:00-13:00 | Lunch | |
| 13:00-14:00 | Talk: presentation of tools use in the practical session | Louis Letourneau and Mathieu Bourgey |
| 14:00-15:00 | Practical: data processing, alignment, SNP detection | Louis Letourneau and Mathieu Bourgey |
| 15:00-15:15 | Coffee Break | |
| 15:15-17:00 | Practical: data processing, alignment, SNP detection | Louis Letourneau and Mathieu Bourgey |
| Day 2 - 19 March 2013 - Materials |
||
| 09:00-11:00 | Talk: Introduction to structural variation and CNV methods and tools | Louis Letourneau and Mathieu Bourgey |
| 11:00-11:15 | Coffee Break | |
| 11:15-11:40 | Talk: Visualization of next generation data and results | Louis Letourneau and Mathieu Bourgey |
| 11:40-12:00 | Structural variation detection tools and how they compare | Louis Letourneau and Mathieu Bourgey |
| 12:00-13:00 | Lunch | |
| 13:00-14:00 | Talk: Introduction and browser demos focusing on a gene, transcripts, and (COSMIC) variants involved in Cancer | Denise Carvalho-Silva |
| 14:00-15:00 | Talk: Data upload with sequence reads | Denise Carvalho-Silva |
| 15:00-15:15 | Coffee Break | |
| 15:15-17:30 | BioMart to pull out gene/variation data associated with a phenotype/cancerous gene & Hands-on exercises | Denise Carvalho-Silva |
| Day 3 - 20 March 2013 - Materials |
||
| 09:00-11:00 | Talk: Trouble shooting and validation of next generation data | Louis Letourneau and Mathieu Bourgey |
| 11:00-11:15 | Coffee Break | |
| 11:15-12:00 | Talk: presentation of tools use in the practical session | Louis Letourneau and Mathieu Bourgey |
| 12:00-13:00 | Lunch | |
| 13:00-15:00 | Practical: Structural variants, CNV, visualization, and free analysis | Louis Letourneau and Mathieu Bourgey |
| 15:00-15:15 | Coffee Break | |
| 15:15-17:30 | Practical: Structural variants, CNV, visualization, and free analysis | Louis Letourneau and Mathieu Bourgey |
| Day 4 - 21 March 2013 - Materials |
||
| 09:00-10:00 | Talk: Introduction to RNA-seq, with an overview of common research questions | Liliana Greger |
| 10:00-10:30 | Talk: Dealing with raw data: QA + filtering | Liliana Greger |
| 10:30-10:45 | Coffee Break | |
| 10:45-12:00 | Practical: Dealing with raw data | Liliana Greger and Mar Gonzales Porta |
| 12:00-13:00 | Lunch | |
| 13:00-14:00 | Talk: Dealing with aligned data: mapping, expression estimation, normalisation, DE | Mar Gonzales Porta |
| 14:00-15:00 | Practical: Dealing with aligned data | Liliana Greger and Mar Gonzales Porta |
| 15:00-15:15 | Coffee Break | |
| 15:15-17:30 | Practical: Dealing with aligned data | Liliana Greger and Mar Gonzales Porta |
| Day 5 - 22 March 2013 - Materials |
||
| 09:00-9:30 | Introduction to networks and pathways | Steve Jupe |
| 10:00-10:30 | Reactome | Steve Jupe |
| 10:30-10:45 | Coffee Break | |
| 10:45-11:15 | Practical: Reactome | Steve Jupe |
| 11:15-12:00 | Reactome Functional Interactors | Steve Jupe |
| 12:00-13:00 | Lunch | |
| 13:00-14:00 | Mining for combinatorial patterns of mutations in large-scale cancer genomics data sets | Francesco Iorio |
| 14:00-15:00 | From patterns of mutations to pathway alterations | Francesco Iorio |
| 15:00-15:15 | Coffee Break | |
| 15:15-17:30 | Tools for the identification of mutual exclusively mutated network modules | Francesco Iorio |
If you require the data files please contact us directly as they are too big to upload onto the web site.
There is a 2 stage registration process for this course. In the first instance, you are required to apply to attend this course, then after the closing date (31 January 2013 at 12:00 midday GMT), all successfull applicants will be sent a link to register their attendance and make the payment for the course.
The registration fee for this event is £250.00, which includes:
- Accommodation and breakfast for 5 nights at Hinxton Hall, The Wellcome Trust Genome Campus, Hinxton - (Check in Sunday 17 March 2013 - Check out Friday 22 March 2013)
- Refreshments and lunch during the course
- Course dinner on Tuesday 19 March 2013 at Jesus College, Cambridge
- Dinner at the Wellcome Trust, Monday 18 March, Wednesday 20 March, Thursday 21 March 2013
- Course materials
- Use of the EBI Training Room computer for the duration of the course
Application is now closed