Overview

Cancer is a disease of the genome. Mutations of genes that regulate cell proliferation and cell death result in uncontrolled growth eventually causing symptoms. During cancer progression, mutations build up that not only affect cell growth, but also can suppress the immune system, increase the chance of metastases and promote genome instability leading to additional malignant mutations.

Characterizing the mutations of malignant tissue has been instrumental for the development of the diagnosis, prognosis and treatment of cancer in the last decades. Cancer is a highly heterogeneous disease, and by knowing the type of mutations, we have a better understanding of the nature of tumors, and can apply precision medicine approaches, like targeted drug and immune therapy.

Cancer variants are somatic, which means that they exist in only a part of the cells in the tissue. Even in a sample of a solid tumor, only a part of the cells contains the driver mutations. This makes analysis of cancer variants more challenging than inherited variants, where we assume (almost) all cells have the same genome.

In this course, you will learn the concepts of calling somatic variants from next generation sequencing data, and the basics of performing cancer variant annotation. The practical work will be mainly based on the GATK4 (Mutect2) pipeline and Ensembl's Variant Effect Predictor (VEP).

The course materials will be on the dedicated GitHub page.

Audience

This intermediate level course is addressed to researchers and clinicians who work with cancer biology and want to get started with performing somatic variant analysis and interpretation of the results.

Learning outcomes

At the end of the course, the participants should be able to:

Understand the difference between germline and somatic variants and the implication of computational analysis
Perform a somatic variant analysis on a paired sample (tumor – normal) with GATK4
Perform a somatic variant annotation with VEP and use the results to filter possible high-impact mutations in the cancer genome

Prerequisites

Knowledge / competencies

Participants should have knowledge in NGS techniques, quality control and alignment to a reference genome, and detection of genomic variants from read alignment to variant calling and annotation.

The competences and knowledge levels required correspond to those taught in courses such as: NGS - Quality Control, Alignment, Visualisation and NGS-Genome Variant Analysis.

Participants should have a basic understanding of working with command line tools on Unix-based systems. You can test your skills with Unix with the quiz here. If you do not feel comfortable with UNIX commands, please take our Unix fundamentals e-learning module.

Technical

Participants should have their own computer with a browser installed (e.g. chrome, firefox, edge), and can access http websites. Test it here: http://httpforever.com/.

Schedule - CET time zone

The schedule and course material will be made available on a dedicated GitHub page.

Application

Registration fees are 100 CHF for academics and 500 CHF for for-profit companies.

While participants are registered on a first come, first served basis, exceptions may be made to ensure diversity and equity, which may increase the time before your registration is confirmed.

Applications will close as soon as the places will be filled up, until 22/11/2024. Deadline for free-of-charge cancellation is set to 29/11/2024. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Venue and Time

This course will be streamed via Zoom.

The course will start at 9:00 and end around 17:00 CET. Precise information will be provided to the participants in due time.

Additional information

Coordination: Diana Marek, SIB Training group.

We will recommend 0.25 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.

Cancer Variant Analysis