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DTSTAMP:20260709T145055Z
UID:7b60fec2-8b12-4ac4-9664-de749699a4cc
DTSTART:20241213T090000Z
DTEND:20241213T170000Z
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\nThe course materials will be on the 
 dedicated GitHub page.\n\n## Audience\nThis intermediate level course is a
 ddressed to researchers and clinicians who work with cancer biology and wa
 nt to get started with performing somatic variant analysis and interpretat
 ion of the results.  \n\n## Learning outcomes\nAt the end of the course\, 
 the participants should be able to: \n\n* Understand the difference betwee
 n germline and somatic variants and the implication of computational analy
 sis \n\n* Perform a somatic variant analysis on a paired sample (tumor –
  normal) with GATK4  \n\n* Perform a somatic variant annotation with VEP a
 nd use the results to filter possible high-impact mutations in the cancer 
 genome \n## Prerequisites\n##### Knowledge / competencies\nParticipants sh
 ould 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.  \n\nThe competences and knowledge leve
 ls required correspond to those taught in courses such as: [NGS - Quality 
 Control\, Alignment\, Visualisation](https://www.sib.swiss/training/course
 /20241120_NGSQC) and [NGS-Genome Variant Analysis](https://www.sib.swiss/t
 raining/course/20240905_NGSGV). \n\nParticipants should have a basic under
 standing 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 comfort
 able with UNIX commands\, please take our Unix fundamentals e-learning mod
 ule. \n##### Technical\nParticipants should have their own computer with a
  browser installed (e.g. chrome\, firefox\, edge)\, and can access http we
 bsites. Test it here: [http://httpforever.com/](http://httpforever.com/). 
  \n\n## Schedule - CET time zone\nThe schedule and course material will be
  made available on a dedicated GitHub page.\n\n## Application\nRegistratio
 n fees are **100 CHF** for academics and **500 CHF** for for-profit compan
 ies. \n\nWhile 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. \n\nApplications 
 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**. Cancel
 lation after this date will not be reimbursed. Please note that participat
 ion in SIB courses is subject to our [general conditions](https://www.sib.
 swiss/training/terms-and-conditions). \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 with
 in 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 informat
 ion will be provided to the participants in due time. \n\n## Additional in
 formation\nCoordination: Diana Marek\, SIB Training group.\n\nWe will reco
 mmend 0.25 ECTS credits for this course (given a passed exam at the end of
  the course).\n\nYou are welcome to register to the SIB courses mailing li
 st to be informed of all future courses and workshops\, as well as all imp
 ortant deadlines using the form [here](https://lists.sib.swiss/postorius/l
 ists/courses.lists.sib.swiss/).\n\nPlease note that participation in SIB c
 ourses is subject to our [general conditions](https://www.sib.swiss/traini
 ng/terms-and-conditions).\n\nSIB abides by the [ELIXIR Code of Conduct](ht
 tps://elixir-europe.org/events/code-of-conduct). Participants of SIB cours
 es are also required to abide 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/20241213_CVANA
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