27-29 April 2026

This comprehensive workshop provides participants with practical skills in cancer genomics analysis, focusing on somatic variant detection and annotation. The course covers the complete workflow from raw sequencing data to the identification of potentially pathogenic mutations in cancer genomes. Through a combination of theoretical lectures and hands-on sessions, participants will learn industry-standard tools and methodologies currently employed in cancer genomics research and precision oncology.

 This course is designed for students and researchers interested in cancer genomics. Participants should have basic familiarity with the command line and some programming experience (preferably R). Basic understanding of genomics and DNA sequencing is recommended but not required.

Course data includes whole-exome sequencing (WES) data from matched tumor-normal cancer cell lines with all reference files (GRCh38, Panel of Normals, gnomAD, and cancer-relevant annotation databases including REVEL, ClinVar) pre-staged.

By the end of this course, participants will be able to:

•    Perform quality control on sequencing data and interpret QC metrics
•    Align reads to a reference genome and assess alignment quality
•    Distinguish between germline and somatic variants from a biological and computational perspective
•    Understand the critical role of matched tumor-normal pairs in cancer genomics
•    Implement a complete somatic variant calling pipeline using GATK4 Mutect2
•    Work with VCF files in R for variant analysis
•    Annotate variants using VEP and interpret the results in a cancer biology context
•    Analyze Variant Allele Frequency (VAF) distributions
•    Filter and prioritize potentially pathogenic mutations based on biological impact
•    Create visualizations of variant characteristics and findings

Daily schedule: 2:00 am to 5:00 PM (Berlin time)

Day 1: Foundations and Data Preparation
•    Cancer genomics fundamentals: somatic vs. germline mutations
•    Sequencing data quality control and preprocessing
•    Read alignment and BAM file analysis
•    Introduction to data formats (FASTQ, BAM, VCF)

Day 2: Somatic Variant Calling with GATK4
•    Principles of somatic variant detection
•    GATK4 Mutect2 pipeline with matched tumor-normal samples
•    Understanding and applying variant filtering strategies
•    Introduction to key resources (Panel of Normals, population databases)

Day 3: Variant Annotation and Interpretation
•    Functional annotation with Ensembl VEP
•    Integration with cancer-relevant databases
•    Variant analysis and prioritization using R
•    Interpretation of variant characteristics including allele frequencies
•    Visualization and reporting strategies