e-learning

Identification of somatic and germline variants from tumor and normal sample pairs

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Abstract

When sequencing genomic material from a human tumor, the underlying clinical or

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

  • What are the specific challenges in somatic variant calling that set it apart from regular diploid variant calling?
  • How can you call variants and classify them according to their presence/absence in/from tumor and normal tissue of the same individual?
  • How can you annotate variants and affected genes with prior knowledge from human genetic and cancer-specific databases to generate clinically relevant reports?

Learning Objectives

  • Call variants and their somatic status from whole-exome sequencing data
  • Annotate variants with a wealth of human genetic and cancer-specific information extracted from public databases
  • Add gene-level annotations and generate reports of annotated somatic and germline variants, loss-of-heterozygosity (LOH) events, and affected genes, ready for interpretation by clinicians

Licence: Creative Commons Attribution 4.0 International

Keywords: Variant Analysis

Target audience: Students

Resource type: e-learning

Version: 15

Status: Active

Prerequisites:

  • Introduction to Galaxy Analyses
  • Mapping
  • Quality Control

Learning objectives:

  • Call variants and their somatic status from whole-exome sequencing data
  • Annotate variants with a wealth of human genetic and cancer-specific information extracted from public databases
  • Add gene-level annotations and generate reports of annotated somatic and germline variants, loss-of-heterozygosity (LOH) events, and affected genes, ready for interpretation by clinicians

Date modified: 2023-11-09

Date published: 2019-03-13

Authors: Wolfgang Maier

Contributors: Wolfgang Maier

Scientific topics: Genetic variation

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