CAS PMO Detailed Program 2022 2023 v1.0
CAS PMO Detailed Program 2022 2023 v1.0
CAS PMO Detailed Program 2022 2023 v1.0
Advanced Studies in
Personalized Molecular
Oncology
Dates
• 4, 5; 25, 26 November 2022 (28h presential teaching).
Location
• Lausanne, CHUV University Hospital.
Main topics
• 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
• Tumor cell proliferation
• Clonal evolution & tumor heterogeneity
Module coordinator
• Prof. Jacqueline Schoumans (CHUV)
Course format
• Lectures, exercises, group discussions and lab visit.
Dates
• 20, 21 January; 3, 4 February 2023 (28h presential teaching).
Location
• Basel, Basel University Hospital.
Main topics
• Sample classification and preparation
• Principles of nucleic acids extraction
• Sequencing platforms and setup
• Understanding gene panels
• Internal / external quality controls
• Laboratory accreditation
• Reporting clinically relevant genomic variants
• Interpreting a molecular profile
Module coordinators
• PD Dr. Christian Ruiz (USB), Dr. Salvatore Piscuoglio (USB), PD Dr. Matthias
Matter (USB)
Course format
• Lectures, exercises, group discussions and lab visit.
• [0h45] Digital Pathology (Prof. Dr. Viktor Közer, University Hospital Zürich)
• [0h45] Molecular Pathology of Breast Cancer (PD Dr. Simone Münst, USB)
• [0h45] Molecular Pathology of the Lung Cancer (PD Dr. Spasenija Savic,
USB)
• [1h] Single cell sequencing (Dr. Guglielmo Roma, GSK, Italy; VIRTUAL)
• [1h] Guidelines for diagnostic reporting (PD Dr. Matthias Matter, USB)
Dates
• 17, 18 March; 31 March, 1 April 2023 (28h presential teaching).
Location
• Lausanne, University of Lausanne.
Main topics
• Data pre-processing
• Read mapping
• Variant calling
• Quality control
• Variant annotation
• Hardware, security, privacy
• Artificial intelligence (AI) basics
• AI current and future applications
Module coordinators
• Dr. Aitana Lebrand (SIB), Valérie Barbié (SIB)
Course format
• Lectures, hands-on, exercises and group discussions.
• [1h] Sequence alignment and read mapping (Dr. Aitana Lebrand, SIB)
I. QC at the variant-level
• [0h30] Example case (Dr. Yann Christinat, HUG/SIB).
• [0h30] Copy number variants (CNVs) and other structural variants (SVs)
(Dr. Yann Christinat, HUG/SIB)
• [1h45] All you need is IT: a study case on all that’s hidden (Florent Tassy
and Valérie Barbié, SIB)
Dates
• 12, 13 May; 26, 27 May 2023 (28h presential teaching).
Location
• Basel, Basel University Hospital.
Main topics
• 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
• Molecular Tumor Board
Module coordinators
• PD Dr. Dr. Sacha Rothschild (USB), PD Dr. Dr. Andreas Wicki (USZ)
Course format
• Lectures, exercises and group discussions.
• [2h] Basic concepts of cancer therapy: (PD Dr. Dr. Sacha Rothschild, USB)
o Surgery, radiation therapy, systemic therapy
o Adjuvant, neoadjuvant, palliative
o Markers for systemic therapy: prognostic, predictive
o Definitions: OS, PFS, ORR, etc.
• [2h] Tumor biology: from molecular biology of cancer to targets for anti-
cancer drugs (Dr. Nicola Miglino, KSBL)
o What are the hallmarks of cancer (Weinstein/Hanahan)?
o What hallmarks are druggable?
o Clinical data for drugs targeting hallmarks of cancer
o Clinical data for markers of benefit in targeted therapies
o Mechanisms of resistance to targeted therapies
• [1h] Overview: what markers can predict outcome of therapies? (PD Dr.
Dr. Andreas Wicki, KSBL)
o Clinical parameters
o Radiology parameters
o Histology
o Immunohistochemistry
o FISH
o Comparative genomic hybridization
o Sequencing of DNA, RNA (genomics, transcriptomics)
o Others
• [2h] How do you read a genomic report as a clinician? (PD Dr. Dr. Sacha
Rothschild, USB)
o Basics: sources of information, databases
o Tips and tricks
o HANDS-ON: interpret bulk DNA sequencing report
• [2h] Overview: drug development in oncology (PD Dr. Dr. Andreas Wicki,
KSBL)
o Preclinical
o Early phase
o Late phase and approval
o Post marketing studies
o Attrition rate
o Clinical trial protocol, role of ethical committees and Swissmedic,
informed consent
o Primary endpoints vs secondary endpoints vs exploratory endpoints
• [1h] Reimbursement: how to get a drug after your test predicts utility (PD
Dr. Dr. Sacha Rothschild, USB)
o DISCUSSION: assurance of equal treatment for all patients
(“off-label” use)
• [2h] Beyond genetics in therapy prediction (PD Dr. Dr. Andreas Wicki,
KSBL)
o Proteomics
o Single cell phenotyping
o Machine-based learning
• [1h] Algorithm trials: how to transform data in a robust prediction (PD Dr.
Dr. Andreas Wicki, KSBL)
University of Basel
Department of Biomedicine
Hebelstrasse 20
CH-4031 Basel
pmo.unibas.ch