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DTSTAMP:20260719T033502Z
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DTSTART:20251212T090000Z
DTEND:20251212T170000Z
DESCRIPTION:## Overview\nCancer is a disease of the genome. Mutations of ge
 nes 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 imm
 une system\, increase the chance of metastases and promote genome instabil
 ity leading to additional malignant mutations.  \n\nCharacterizing the mut
 ations of malignant tissue has been instrumental for the development of th
 e diagnosis\, prognosis and treatment of cancer in the last decades. Cance
 r 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.  \n
 \nCancer 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 pa
 rt of the cells contains the driver mutations. This makes analysis of canc
 er variants more challenging than inherited variants\, where we assume (al
 most) all cells have the same genome.  \n\nIn 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 practic
 al work will be mainly based on the GATK4 (Mutect2) pipeline and Ensembl's
  Variant Effect Predictor (VEP).  \n\n\n## Audience\nThis course is design
 ed for PhD students\, clinicians\, postdoctoral and other researchers in t
 he life sciences from both academia and industry who work with cancer biol
 ogy and want to get started with performing somatic variant analysis and i
 nterpretation of the results.  \n\n\n## Learning outcomes\nAt the end of t
 he course\, the participants should be able to: \n\n* **Understand** the d
 ifference between germline and somatic variants and the implication of com
 putational analysis \n\n* **Perform** a somatic variant analysis on a pair
 ed sample (tumor – normal) with GATK4  \n\n* **Perform** a somatic varia
 nt annotation with VEP and use the results to filter possible high-impact 
 mutations in the cancer genome \n\n\n## Prerequisites\n### Knowledge / com
 petencies\nParticipants should have knowledge in NGS techniques\, quality 
 control and alignment to a reference genome\, and detection of genomic var
 iants from read alignment to variant calling and annotation.  \n\nIdeally 
 participants have already completed courses such as: Introduction to Seque
 ncing Data Analysis and NGS-Genome Variant Analysis\, or have equivalent k
 now-how experience.\nYou can look at the materials from the past SIB’s N
 GS courses [here](https://sib-swiss.github.io/sequencing-data-analysis-tra
 ining/latest/) and [here](https://sib-swiss.github.io/NGS-variants-trainin
 g/latest/) for a refresh.\n\nParticipants should have a basic understandin
 g of working with command line tools on Unix-based systems. You can test y
 our skills with Unix with the quiz here. If you do not feel comfortable wi
 th UNIX commands\, please take our Unix fundamentals e-learning module. \n
 ### Technical\nParticipants should have their own computer with any modern
  browser installed (e.g. chrome\, firefox\, edge)\, with an access to http
  websites (test it here: [http://httpforever.com/](http://httpforever.com/
 )\, and with a stable Internet access. We will use cloud-based AWS infrast
 ructure \, which will serve as a remote work environment for all participa
 nts. At the end of the course\, the remote environment will be deleted. In
 formation on local installation is also provided in the course materials.\
 n\n## Schedule - CET time zone\nThe schedule and course material is availa
 ble on a dedicated [GitHub page](https://sib-swiss.github.io/cancer-varian
 ts-training/course_schedule.html).\n\n## Application\nRegistration fees ar
 e **100 CHF** for academics and **500 CHF** for for-profit companies. \n\n
 While participants are registered on a first come\, first served basis\, e
 xceptions may be made to ensure diversity and equity\, which may increase 
 the time before your registration is confirmed. \n\nApplications will clos
 e as soon as the places will be filled up\, until **28/11/2025**. Deadline
  for free-of-charge cancellation is set to **28/11/2025**. Cancellation af
 ter this date will not be reimbursed.\n\nYou 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 withi
 n 5 days. \n\n## Venue and Time\nThis course will be streamed via Zoom.\n\
 nThe course will start at 9:00 and end around 17:00 CET. Precise informati
 on will be provided to the participants in due time. \n\n## Additional inf
 ormation\nCoordination: Grégoire Rossier\, SIB Training group.\n\nHelpers
 : Deepak Tanwar and Aparna Pandey\n\nWe will recommend 0.25 ECTS credits f
 or this course (given a passed exam at the end of the course).\n\nYou 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 th
 e form [here](https://lists.sib.swiss/postorius/lists/courses.lists.sib.sw
 iss/).\n\nPlease note that participation in SIB courses is subject to our 
 [general conditions](https://www.sib.swiss/training/terms-and-conditions).
 \n\nSIB abides by the [ELIXIR Code of Conduct](https://elixir-europe.org/e
 vents/code-of-conduct). Participants of SIB courses are also required to a
 bide by the same code.\n\nFor more information\, please contact [training@
 sib.swiss](mailto://training@sib.swiss).
SUMMARY:Cancer Variant Analysis
URL;VALUE=URI:https://www.sib.swiss/training/course/20251212_CVANA
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