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HP-F1: Molecular, Genetic and Bioinformatic Approaches in Cancer Research

Type: Practical Course with Student Seminars


Date: 20. November - 15. December 2023 (no course in week 4.-8. Dec.)

Introduction, delivery of scripts and literature: date and mode/location t.b.a.

Locations: DKFZ Teaching Lab, various DKFZ Main Building Seminar Rooms

Hosts/Supervisors: Maïwen Caudron-Herger (responsible organizer); David Jones; Marc Zuckermann



1. Analysis of mass spectrometry data on protein-RNA interactions using a major bioinformatic tool

2. Investigation of tumor heterogeneity using single-nucleus RNA sequencing

3. Generation and identification of CRISPR nucleases in oncology


Topic 1 - Organizer: Maïwen Caudron-Herger

The analysis of a mass spectrometry dataset linked to protein-RNA interactions will serve as a basis to introduce simple programming notions in R ranging from reading a file to the production of graphics. Simple notions of biostatistics will be introduced and implemented. The results of the proteomic analysis and their meaning will be discussed.


Topic 2 - Organizer: David Jones

The course (wet- & dry-lab hybrid) will give an introduction to the use of single cell transcriptomic methods for investigating tumor heterogeneity. The students will learn to extract intact nuclei from frozen tissues and prepare libraries for next-gen sequencing. For time-reasons, pre-prepared datasets will then be used to introduce bioinformatic analytical methods. Potential methods for validation of target genes will be discussed and practically demonstrated.


Topic 3 - Organizer: Marc Zuckermann

The course will introduce multiple uses of the CIRSPR-Cas9 system in oncology. The students will learn to design, clone and validate Cas9-gRNA combinations to target tumor suppressor genes as well as oncogenic driver mutations specifically, using online tools, standard cloning techniques and cell culture assays.

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