PhD Project in Spatial
Transcriptomics

(Ref-No. 2022-0152)

The laboratory of Dr. Moritz Gerstung (Division of Artificial Intelligence in Oncoclogy) at the German Cancer Research Center is looking for a PhD candidate for a project in spatial genomics. The group studies cancer evolution using a combination of AI analysis and new experimental technologies [1,2]. We have recently co-developed experimental protocols to detect mutations in tissue sections which map how cancers have grown in their tissue context [3]. This method, termed base specific in situ sequencing (BaSISS) extends the Cartana/10x ISS protocol. The BaSISS protocol combines sequencing of a tumour to identify mutations and localises these variants in a tumour section with single molecule padlock probes, which are interrogated by cyclic fluorescence microscopy. This generates signals from 100,000s of cells in a tissue, which are assembled into maps of subclonal growth. The protocols also allow for measuring the histopathological and transcriptomic changes acquired during tumour progression.

Job description:
We are looking for an experimentally skilled PhD candidate to apply these spatial genomics technologies to study the evolution of sarcomas and other cancer types. You will work alongside other lab members and in collaboration with the Single-cell Open Lab [4] to pursue our efforts to use spatial genomics for studying cancer evolution in our new lab at DKFZ [5] which opened in September 2021. Being part of an international interdisciplinary team working both experimentally and computationally will offer you a comprehensive training and opportunities to broaden your horizon in many ways. Furthermore, you will have the opportunity to take full advantage of all the training and social activities the DKFZ International PhD Program has to offer [6]. Your responsibilities:

• Implementation and application of BaSISS and general ISS experiments
• Run 10x visium spatial transcriptomics arrays on fresh and fixed tissues
• Analysis of the resulting data sets to map clonal evolution in tissues 
• Integrate single-cell RNA sequencing data to understand clone-specific expression changes and interactions of cancer and normal cells

Further information:

1. Fu, Y. et al. Pan-cancer computational histopathology reveals mutations, tumor composition and prognosis. Nature Cancer 1, 800–810 (2020)
2. Gerstung, M. et al. The evolutionary history of 2,658 cancers. Nature 578, 122–128 (2020)
3. Lomakin, A. et al. Spatial genomics maps the structure, character and evolution of cancer clones. bioRxiv (2021) doi:10.1101/2021.04.16.439912
4. https://www.dkfz.de/en/single-cell-sequencing/open-lab.html
5. https://www.dkfz.de/en/kuenstliche-intelligenz-in-der-onkologie/index.php 
6. https://www.dkfz.de/en/phd-program/

Your profile:
Key skills:

• An MSc in biological sciences or related field
• Experience with tissue preservation (e.g. fixation, cryo-preservation) and sectioning including both paraffin embedded and frozen tissue material
• Experience in fluorescence microscopy of cells or tissues
• Excellent communication skills in English and the ability to work effectively within a team 

Desirable skills:

• Experience with immunohistochemistry and in situ hybridization
• Knowledge of image data pre-processing
• Ability to test, implement and troubleshoot new techniques and protocols
• Attention to detail and record keeping for sample and experimental tracking

We offer:

• Interesting, versatile workplace
• International, attractive working environment
• Campus with modern state-of-the-art infrastructure
• Access to international research networks
• Doctoral student payment including social benefits
• Flexible working hours
• Comprehensive training and mentoring program through the Helmholtz International Graduate School

The position is limited to 3 years with the possibility of prolongation.

Important notice:
The DKFZ is subject to the regulations of the Infection
Protection Act (IfSG). As a consequence, only persons who
present proof of immunity against measles as well as against
COVID-19 may work at the DKFZ.