ishamada/cancergenomicstranscriptomics

Cancer genomics and transcriptomic course - EMBL-EBI (2023) - balqees

The section of this course will be split into two main practical sessions. Both lectures will focus on detecting short variants (single nucleotide variants, as well as small insertions and deletions) in cancer, performing mutational signature analysis and understanding the clonal architecture in tumours.

1. Alignment and SNV analysis

In this practical session (find the theory here), you will be guided through the process of detecting single nucleotide variation in cancer. You will gain hands-on experience in analyzing short-read DNA sequencing data, covering the entire workflow from quality control and alignment to variant calling and variant annotation. The main core of this lecture is split into three parts:

1. Alignment
2. Somatic variant calling
3. Variant annotation

By the end of this session, you will be able to:

• Align short-read data against a reference genome
• Recall the steps of a tumour-pair SNV pipeline

2. Mutational signatures and clonal population structure analysis in cancer genomes

During this second practice session, we will focus on the detection and interpretation of mutational signatures in real samples. You will learn how to identify and analyse these signatures. Additionally, we will explore the interpretation of the clonality of somatic mutations to gain insights into the clonal structure of cancer genomes. Find all the theory here. The main core of this lecture is split into two parts:

1. Mutational signature analysis
   • De novo mutational signature extraction. (Download this file and open it in the browser)
   • Refitting with known signatures. (Download this file and open it in the browser)
2. Understanding cancer cell fraction. (Download this file and open it in the browser)

By the end of this session, you will:

• Have a comprehensive understanding of mutational signatures and the calculations of cancer cell fractions.

Author and contact

Author: Francesc Muyas Remolar, PhD (EMBL-EBI)

If you have any comments or questions:

Francesc Muyas: [email protected]