BEGIN:VCALENDAR VERSION:2.0 PRODID:icalendar-ruby CALSCALE:GREGORIAN BEGIN:VEVENT DTSTAMP:20260715T193439Z UID:7fa44116-6e5a-4621-bfa6-a616c035cef0 DTSTART:20261029T090000Z DTEND:20261103T170000Z DESCRIPTION:Please note that this 1-day course will be streamed over 2 half -days\, in the afternoon of the following dates:\n* 29 October 2026\n* 03 November 2026\n\n\n## Overview\n\nCancer is a disease of the genome. Mutat ions of genes that regulate cell proliferation and cell death result in un controlled growth eventually causing symptoms. During cancer progression\, mutations build up that not only affect cell growth\, but also can suppre ss the immune system\, increase the chance of metastases and promote genom e instability leading to additional malignant mutations. \n\nCharacterizi ng the mutations of malignant tissue has been instrumental for the develop ment of the diagnosis\, prognosis and treatment of cancer in the last deca des. 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 th erapy. \n\nCancer variants are somatic\, which means that they exist in o nly 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 analys is of cancer variants more challenging than inherited variants\, where we assume (almost) all cells have the same genome. \n\nIn this course\, you will learn the concepts of calling somatic variants from next generation s equencing data\, and the basics of performing cancer variant annotation. T he practical work will be mainly based on the GATK4 (Mutect2) pipeline and Ensembl's Variant Effect Predictor (VEP). \n\n## Audience\n\nThis course is designed for PhD students\, clinicians\, postdoctoral and other resear chers in the life sciences from both academia and industry who work with c ancer biology and want to get started with performing somatic variant anal ysis and interpretation of the results. \n\n## Learning outcomes\n\nAt th e end of the course\, the participants should be able to:\n\n* **Understan d** the difference between germline and somatic variants and the implicati on of computational analysis \n\n* **Perform** a somatic variant analysis on a paired sample (tumor – normal) with GATK4 \n\n* **Perform** a soma tic variant annotation with VEP and use the results to filter possible hig h-impact mutations in the cancer genome \n\n## Prerequisites\n\n### Knowle dge / competencies\n\nParticipants 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. \ n\nTo get the most out of this course\, you should meet the learning outco mes of [Introduction to Sequencing Data Analysis](https://www.sib.swiss/tr aining/course/ISEDA) and [NGS - Genome Variant Analysis](https://www.sib.s wiss/training/course/NGSGV) courses or have equivalent know-how experience .\n\nParticipants should have a basic understanding of working with comman d line tools on UNIX-based systems. You can test your skills with Unix wit h the quiz here. If you do not feel comfortable with UNIX commands\, pleas e take our UNIX fundamentals e-learning module. \n\n\n### Technical\n\nPar ticipants 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 sta ble Internet access. We will use cloud-based AWS infrastructure \, which w ill serve as a remote work environment for all participants. At the end of the course\, the remote environment will be deleted. Information on local installation is also provided in the course materials.\n\n\n## Schedule – CE(S)T time zone\nThe schedule and course material is available on a d edicated [GitHub page](https://sib-swiss.github.io/cancer-variants-trainin g/course_schedule.html).\n\n## Application\n\nThe registration fees for ac ademics are **100 CHF** and **500 CHF** for for-profit companies.\n\nWhile participants are registered on a first come\, first served basis\, except ions may be made to ensure diversity and equity\, which may increase the t ime before your registration is confirmed.\n\nApplications will close on * *15/10/2025** or as soon as the places will be filled up. Cancellation aft er **15/10/2025** will not be reimbursed. Please note that participation i n SIB courses is subject to our [general conditions](https://www.sib.swiss /legal-documents).\n\nYou will be informed by email of your registration c onfirmation. Upon reception of the confirmation email\, participants will be asked to confirm attendance by paying the fees within **5 working days* *.\n\n## Venue and Time\n\nPlease note that this 1-day course will be stre amed over 2 half-days\, from 13:00 to 17:00 CET on the following dates:\n* 29 October 2026\n* 03 November 2026\n\nPrecise information will be provid ed to the registered participants in due time.\n\n## Additional informatio n\n\nCoordination: Diana Marek\, SIB Training group.\n\nA **Certificate of Attendance** will be sent provided you were present at the course\, where as a **Certificate of Achievement** recommending 0.25 ECTS will be sent pr ovided you passed the exam.\n\nYou are welcome to register to the SIB cour ses mailing list to be informed of all future courses and workshops\, as w ell as all important deadlines using the form [here](https://lists.sib.swi ss/mailman/listinfo/courses).\n\nSIB abides by the [ELIXIR Code of Conduct ](https://elixir-europe.org/events/code-of-conduct). Participants of SIB c ourses are also required to abide by the same code.\n\nFor more informatio n\, please contact [training@sib.swiss](mailto://training@sib.swiss). SUMMARY:Cancer Variant Analysis URL;VALUE=URI:https://www.sib.swiss/training/course/20261029_CVANA END:VEVENT END:VCALENDAR