Analysis of cancer genomes using R and bioinformatic tools
On this course, which has been divided into five segments, you will learn how to process “raw” sequencing reads, and call the three most fundamental types of mutations found in cancer genomes: somatic single nucleotide variants, insertions and deletions, and chromosome copy aberrations. The background, theory, and main tools available will all be covered in the first part of the course. In the final segments you will learn advanced methods for sample quality control and tumour subclonal deconvolution, the task in which somatic variants are used to determine the tumour architecture (i.e., how many clones constitute the cancer) from an evolutionary perspective. Together this course will prepare any would be bioinformatician for further education or employment within a cancer research laboratory.
TARGET AUDIENCE AND ASSUMED BACKGROUND
For the theoretical parts:
- basic understanding of biology and genomics in the context of cancer;
- basic understanding of statistics and data analysis.
Appropriate refreshers will be given within each lesson, where appropriate.
For the practical parts:
- basic knowledge of the UNIX shell processes and commands, including BASH shell scripting;
- ability to write R code with standard packages (dplyr, ggplot) and run it in RStudio
- Proficiency beginning-to-end with a prototype cancer genomics pipeline for bulk sequencing (how to go from the sequencer outputs to somatic calls)
- Proficiency in cancer evolution analyses from bulk sequencing (how to go from somatic calls to tumour clones)
- Working knowledge of some state-of-the-art bioinformatics tools and R packages for cancer genomics