Applied Oncobiology

Instance: 2020/2021 - 2S (of 08-02-2021 to 31-07-2021)

Cycles of Study/Courses

Teaching language

Objectives

Tumor biology and genetics

   Describe the mechanisms yielding to genetic variation, and be familiar with the various types of genetic variants.

   Distinguish hereditary genetic anomalies from acquired genetic anomalies.

   Discuss the advantages and limitations of different genetic laboratory methodologies for diagnostic testing.

   Demonstrate how to interpret non-hotspot mutations using public databases and taking into account overall genomic aberrations and clonal evolution.

   Be aware of ethical implications of incidental genetic findings.

Applied oncobiology

   Describe main intracellular signaling pathways in solid tumors and molecular aberrations hampering this signaling.

   Get detailed knowledge of immunological mechanisms and how these may be used to optimize therapeutic approaches.

   Get a basic understanding of the principles underlying the design and analysis of clinical trials in oncology.

   Understand the importance of predictive markers in molecular oncology.

   Get familiar with the most frequent molecular aberrations in solid tumors and routinely used targeted therapies.

Bioinformatics

   Communicate efficiently with bioinformaticians.

   Describe a bioinformatics analysis pipeline to call mutations from NGS data.

   Perform quality control at the run, read and variant levels.

   Use off-the-shelf bioinformatics tools to annotate and support the interpretation of variants.

   Consider hardware, security and privacy issues when managing omics data.

   Understand how artificial intelligence contributes to and will further impact personalized oncology.

Molecular pathology

   Understand the basics (procedures and rules) of an accredited clinical laboratory.

   Gain knowledge about different types of specimens (e.g. tissue biopsy, cytology, resections).

   Get familiar with all the steps that lead from samples collection to final molecular report generation along with all possible bottlenecks.

   Have an overview about the currently used technological platforms in molecular diagnostics (comparison with the research setting).

   Get familiar with the most common clinically relevant variants along with their interpretation and classification system.

Learning outcomes and competences

Tumor biology and genetics

   Describe the mechanisms yielding to genetic variation, and be familiar with the various types of genetic variants.

   Distinguish hereditary genetic anomalies from acquired genetic anomalies.

   Discuss the advantages and limitations of different genetic laboratory methodologies for diagnostic testing.

   Demonstrate how to interpret non-hotspot mutations using public databases and taking into account overall genomic aberrations and clonal evolution.

   Be aware of ethical implications of incidental genetic findings.

Applied oncobiology

   Describe main intracellular signaling pathways in solid tumors and molecular aberrations hampering this signaling.

   Get detailed knowledge of immunological mechanisms and how these may be used to optimize therapeutic approaches.

   Get a basic understanding of the principles underlying the design and analysis of clinical trials in oncology.

   Understand the importance of predictive markers in molecular oncology.

   Get familiar with the most frequent molecular aberrations in solid tumors and routinely used targeted therapies.

Bioinformatics

   Communicate efficiently with bioinformaticians.

   Describe a bioinformatics analysis pipeline to call mutations from NGS data.

   Perform quality control at the run, read and variant levels.

   Use off-the-shelf bioinformatics tools to annotate and support the interpretation of variants.

   Consider hardware, security and privacy issues when managing omics data.

   Understand how artificial intelligence contributes to and will further impact personalized oncology.

Molecular pathology

   Understand the basics (procedures and rules) of an accredited clinical laboratory.

   Gain knowledge about different types of specimens (e.g. tissue biopsy, cytology, resections).

   Get familiar with all the steps that lead from samples collection to final molecular report generation along with all possible bottlenecks.

   Have an overview about the currently used technological platforms in molecular diagnostics (comparison with the research setting).

   Get familiar with the most common clinically relevant variants along with their interpretation and classification system.

Working method

Program

Tumor biology and genetics

   Basic cytogenetics and molecular genetics

   Hereditary vs. acquired genetics

   Genetic recombination, DNA damage and repair

   Solid tumors and hematological malignancies

   Genetic predisposition to cancer

   Diagnostic genetic testing

   Clonal evolution & tumor heterogeneity

Applied oncobiology

   Tumor Physiology

   Tumor Immunology

   Cancer Statistics and Epidemiology

   Prognostic and Predictive Markers

   Targeted Therapies in Clinical Oncology

   Risks / probabilities for the interpretation of genetic results and counseling

   Clinical Trials in Molecular Oncology

Bioinformatics

   Data pre-processing

   Read mapping

   Variant calling

   Quality control

   Variant annotation

   Hardware, security, privacy

Molecular pathology

   Sample classification and preparation

   Principles of nucleic acids extraction

   Sequencing platforms and setup

   Understanding gene panels

   Internal / external Quality controls

   Laboratory accreditation

   Reporting genomic variants

   Interpreting a molecular profile

Mandatory literature

Teaching methods and learning activities

keywords

Evaluation Type

Assessment Components

Amount of time allocated to each course unit

Eligibility for exams

Calculation formula of final grade